Re: [AMBER] AMBER Digest, Vol 1160, Issue 1

From: Sohag Biswas <cy13p1001.iith.ac.in>
Date: Tue, 17 Mar 2015 14:09:53 +0530

Thanks you Hannes, David and FyD for valuable suggestions.

On Tue, Mar 17, 2015 at 12:30 AM, <amber-request.ambermd.org> wrote:

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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Nuclicacid forcefield in AMBER (mish)
> 2. Re: RNA's sugar modification (Bill Ross)
> 3. Re: RNA's sugar modification (Bill Ross)
> 4. Re: Nuclicacid forcefield in AMBER (David A Case)
> 5. Re: set command and VMD (David A Case)
> 6. ** No torsion terms (Evans, Shalton)
> 7. Re: [q4md-fft] Modify RNA's sugar and adding partial charges (FyD)
> 8. Using WHAM to get 3D free energy surface in AMBER12 (Wang Moye)
> 9. facing problem to create a prmtop file for oxonium cation
> (Sohag Biswas)
> 10. diisopropylethylene parameter (Jennifer Vo)
> 11. Re: finding angles (Vijay Achari)
> 12. Re: facing problem to create a prmtop file for oxonium cation
> (Hannes Loeffler)
> 13. Re: diisopropylethylene parameter (Hannes Loeffler)
> 14. Re: facing problem to create a prmtop file for oxonium cation
> (David A Case)
> 15. Re: Using WHAM to get 3D free energy surface in AMBER12
> (Jason Swails)
> 16. Re: facing problem to create a prmtop file for oxonium cation
> (FyD)
> 17. Re: Decomposition of the MMGBSA based on multi trajectory
> input (James Starlight)
> 18. Re: Decomposition of the MMGBSA based on multi trajectory
> input (James Starlight)
> 19. organic molecule (Lara rajam)
> 20. Per-residue decomposition energy MMGBSA.py (maryam azimzadehirani)
> 21. Re: finding angles (Daniel Roe)
> 22. Re: organic molecule (Jason Swails)
> 23. Re: Per-residue decomposition energy MMGBSA.py (Jason Swails)
> 24. Re: Evaluating hydrogen boding lifetime (Vijay Achari)
> 25. ante-mmpbsa.py: problem with the mask syntax (George Tzotzos)
> 26. Re: finding angles (Vijay Achari)
> 27. Re: finding angles (Jason Swails)
> 28. Re: ante-mmpbsa.py: problem with the mask syntax (Kenneth Huang)
> 29. Re: ante-mmpbsa.py: problem with the mask syntax (Jason Swails)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 15 Mar 2015 20:12:49 +0100
> From: mish <smncbr.gmail.com>
> Subject: [AMBER] Nuclicacid forcefield in AMBER
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFxStkKNqtkTF9=6c9i1rCpiO-=
> DOum-yZRqJATjKWLv3NnHpQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> I would like to know about some appropriate force-field in AMBER to play
> with the thermodynamics of nucleobases binding to proteins? I am very new
> to simulations of nucleic acids, so have not much idea, which ff to start
> with. There are many articles using certain versions of GROMOS, but I am
> not aware of such developments after AMBER-99 in AMBER community. If there
> are some advanced ff that can be used for simulation of single nucleobase
> binding to proteins using implicit solvent models?
>
> Best,
> Mish
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 15 Mar 2015 13:13:20 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] RNA's sugar modification
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <1he88orbgibcpf5w4b2a2bbm.1426450400362.email.android.com>
> Content-Type: text/plain; charset=utf-8
>
> It sounds like you need to make your own residue templates with the
> modified sugars. For this you need to probably adjust atom types, so
> reading force field paper(s) would be in order.
>
> You could make a copy of each residue, giving it a suitable name, delete
> the bond, edit selected atoms to set type, then saveamberprep to save the
> templates. Then loadpdb with a pdb having the new residue names and the
> desired conformation. Tutorials should lay this out in more detail.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: jacob wick <
> jacobwick.la.gmail.com> </div><div>Date:03/15/2015 11:05 AM (GMT-08:00)
> </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject:
> [AMBER] RNA's sugar modification </div><div>
> </div>Hi all,
> I have downloaded a RNA molecule pdb from Nucleic acid databse. When I am
> trying to modify its sugar ring in xleap ( as I want to cleave its c2' -
> c3' bond), loading it again in leap giving me the unmodified structure back
> (I guess leap is adding the modified residues back to the residue
> tamplate). Please suggest how can I modify all sugar ring present in the
> RNA.
>
> Thanks in advance,
> Jac
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------
>
> Message: 3
> Date: Sun, 15 Mar 2015 13:17:57 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] RNA's sugar modification
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <4jwg0cw0fj6u2gxbsf6c70xe.1426450677172.email.android.com>
> Content-Type: text/plain; charset=utf-8
>
> PS - I think savemol2 or similar is more up-to-date than saveamberprep.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Bill Ross <
> ross.cgl.ucsf.edu> </div><div>Date:03/15/2015 1:13 PM (GMT-08:00)
> </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject:
> Re: [AMBER] RNA's sugar modification </div><div>
> </div>It sounds like you need to make your own residue templates with the
> modified sugars. For this you need to probably adjust atom types, so
> reading force field paper(s) would be in order.
>
> You could make a copy of each residue, giving it a suitable name, delete
> the bond, edit selected atoms to set type, then saveamberprep to save the
> templates. Then loadpdb with a pdb having the new residue names and the
> desired conformation. Tutorials should lay this out in more detail.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: jacob wick <
> jacobwick.la.gmail.com> </div><div>Date:03/15/2015 11:05 AM (GMT-08:00)
> </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject:
> [AMBER] RNA's sugar modification </div><div>
> </div>Hi all,
> I have downloaded a RNA molecule pdb from Nucleic acid databse. When I am
> trying to modify its sugar ring in xleap ( as I want to cleave its c2' -
> c3' bond), loading it again in leap giving me the unmodified structure back
> (I guess leap is adding the modified residues back to the residue
> tamplate). Please suggest how can I modify all sugar ring present in the
> RNA.
>
> Thanks in advance,
> Jac
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------
>
> Message: 4
> Date: Sun, 15 Mar 2015 20:33:34 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Nuclicacid forcefield in AMBER
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150316003334.GC43334.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Sun, Mar 15, 2015, mish wrote:
> >
> > I would like to know about some appropriate force-field in AMBER to play
> > with the thermodynamics of nucleobases binding to proteins? I am very new
> > to simulations of nucleic acids, so have not much idea, which ff to start
> > with. There are many articles using certain versions of GROMOS, but I am
> > not aware of such developments after AMBER-99 in AMBER community. If
> there
> > are some advanced ff that can be used for simulation of single nucleobase
> > binding to proteins using implicit solvent models?
>
> You could first create units that just have the nucleobase. I'd suggest
> starting with the nucleosides, removing the sugar part that you don't
> want, and capping the N1 or N9 position with a methyl or whatever group
> matches the experimental situation you with to simulate. If you started
> from ff14SB, you would then have a nucleobase parameterized in way that is
> consistent with the way proteins are parameterized.
>
> Of course, if you know that GROMOS force fields have been specifically
> tested for this sort of interaction, you may wish to follow that lead. A
> lot depends on what you wish to do with the results. Don't expect great
> accuracy for nucleobase-protein thermodynamics using implicit solvent
> models, but poses (geometries) might be of use.
>
> ...good luck....dac
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 15 Mar 2015 20:45:43 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] set command and VMD
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150316004543.GD43334.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=utf-8
>
> On Sat, Mar 14, 2015, Arjun Sharma wrote:
> >
> > I?m trying to merge two polymer fragments into one. I use ?set"
> > command to specify head and tail of two fragments and use ?bond? or
> > ?sequence? command to combine them. The problem is when I try to
> > visualize this merged fragment in VMD, I see that for some reason VMD
> > considers atom # 1 as atom # 0.
>
> I don't think this has anything to do with Amber. VMD starts counting
> atoms
> from 0, not from 1.
>
> >
> > My other question is when I use the ?set command? in tleap as shown
> below
> >
> > >set POLA tail POLA.1.C1
> > >set POLB head POLB.2.C1
> > The value must be of the type: Atom
> > Why can?t use the POLB fragment as residue 2 since it will be
> > residue 2 in the merged fragment ? It works when I use "set POLB head
> > POLB.1.C1?
>
> The fact that POLB be "will be" residue 2 in some future molecule is not
> relevant, (and there is no way that LEaP would know what you plan to do
> later
> on.) As it stands, POLB has one residue, which is residue number 1.
>
> The two issues you raise are not related, as far as I can see.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 16 Mar 2015 00:57:30 +0000
> From: "Evans, Shalton" <shalton.ccs.msstate.edu>
> Subject: [AMBER] ** No torsion terms
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <de863de23ef648bda62a124638b4f588.mail06.ad.msstate.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello All,
>
>
> Im trying to create the parameter files of a half cell lithium battery.
> The molecules involved are Propylene Carbonate, Ethylene Carbonate, PF6-,
> Graphitic Sheets and Lithium. I previously had problems with the graphite
> and thanks to you guys I was able to fix it. Now, there seems to be another
> problem with the Graphic Sheets. I will go through the method to show what
> I did.
>
>
> Since the Graphite is the only element I'm having problems with, I will
> show the .frcmod file for it.
>
>
> I created the file as follows:
>
> parmchk -i gra_test.mol2 -f mol2 -o frcmod
>
>
> the resulting file and its contents:
>
>
> gra_test.frcmod
>
> remark goes here
>
> MASS
>
>
> BOND
>
>
> ANGLE
>
>
> DIHE
>
> ca-ca-cc-cc 1 2.550 180.000 2.000 same as X
> -c2-ca-X
>
> ca-ca-cc-ha 1 2.550 180.000 2.000 same as X
> -c2-ca-X
>
> cc-cc-c2-ha 1 6.650 180.000 2.000 same as X
> -c2-ce-X
>
> ca-cc-c2-ha 1 6.650 180.000 2.000 same as X
> -c2-ce-X
>
> ca-ca-cc-c2 1 2.550 180.000 2.000 same as X
> -c2-ca-X
>
>
> IMPROPER
>
> ca-ca-ca-ha 1.1 180.0 2.0 General
> improper torsional angle (2 general atom types)
>
> ca-ca-ca-ca 1.1 180.0 2.0 Using default
> value
>
> ca-ca-ca-cc 1.1 180.0 2.0 Using default
> value
>
> ca-cc-cc-ha 1.1 180.0 2.0 Using default
> value
>
> c2-ca-cc-cc 1.1 180.0 2.0 Using default
> value
>
> cc-ha-c2-ha 1.1 180.0 2.0 Using default
> value
>
>
> NONBON
>
>
>
> I continued on to leap to attempt the generation of the parameter files
> for the half lithium battery cell as follows.
>
>
> $AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/prep to search path.
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/lib to search path.
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/parm to search path.
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/cmd to search path.
>
> -s: Ignoring startup file: leaprc
>
> -f: Source /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.ff99SB.
>
>
> Welcome to LEaP!
>
> Sourcing: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.ff99SB
>
> Log file: ./leap.log
>
> Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/parm99.dat
>
> Reading title:
>
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
>
> Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/frcmod.ff99SB
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> Modification/update of parm99.dat (Hornak & Simmerling)
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_nucleic94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_amino94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_aminoct94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_aminont94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/ions94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/solvents.lib
>
> > source leaprc.gaff
>
> ----- Source: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff
>
> ----- Source of /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff done
>
> Log file: ./leap.log
>
> Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/gaff.dat
>
> Reading title:
>
> AMBER General Force Field for organic mol., add. info. at the end (June,
> 2003)
>
> > loadoff PCA.lib
>
> Loading library: ./PCA.lib
>
> > loadoff ECA.lib
>
> Loading library: ./ECA.lib
>
> > loadoff PCB.lib
>
> Loading library: ./PCB.lib
>
> > loadoff GRA.lib
>
> Loading library: ./GRA.lib
>
> > loadoff PF6.lib
>
> Loading library: ./PF6.lib
>
> > min_rep=loadpdb min_rep.pdb
>
> Loading PDB file: ./min_rep.pdb
>
> -- residue 1: duplicate [C138] atoms (total 2)
>
> -- residue 2: duplicate [C138] atoms (total 2)
>
> -- residue 3: duplicate [C138] atoms (total 2)
>
> -- residue 4: duplicate [C138] atoms (total 2)
>
>
> Warning: Atom names in each residue should be unique.
>
> (Same-name atoms are handled by using the first
>
> occurrence and by ignoring the rest.
>
> Frequently duplicate atom names stem from alternate
>
> conformations in the PDB file.)
>
>
> Added missing heavy atom: .R<GRA 1>.A<C135 195>
>
> Added missing heavy atom: .R<GRA 2>.A<C135 195>
>
> Added missing heavy atom: .R<GRA 3>.A<C135 195>
>
> Added missing heavy atom: .R<GRA 3>.A<C137 163>
>
> Added missing heavy atom: .R<GRA 4>.A<C135 195>
>
> Added missing heavy atom: .R<PCB 5>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 7>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 9>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 11>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 13>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 15>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 17>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 19>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 21>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 23>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 25>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 27>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 69>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 71>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 73>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 75>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 77>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 79>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 81>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 83>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 85>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 87>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 89>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 91>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 159>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 161>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 163>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 165>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 167>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 169>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 171>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 173>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 175>.A<C4 9>
>
> Added missing heavy atom: .R<PCB 177>.A<C4 9>
>
> total atoms in file: 2465
>
> Leap added 175 missing atoms according to residue templates:
>
> 39 Heavy
>
> 136 H / lone pairs
>
> > saveamberparm min_rep min_rep.prmtop min_rep.inpcrd
>
> Checking Unit.
>
> WARNING: There is a bond of 6.368147 angstroms between:
>
> ------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C140 168>
>
> WARNING: There is a bond of 6.355855 angstroms between:
>
> ------- .R<GRA 1>.A<C138 165> and .R<GRA 1>.A<C139 166>
>
> WARNING: There is a bond of 8.339007 angstroms between:
>
> ------- .R<GRA 1>.A<C137 163> and .R<GRA 1>.A<C138 165>
>
> WARNING: There is a bond of 6.370549 angstroms between:
>
> ------- .R<GRA 2>.A<C138 165> and .R<GRA 2>.A<C140 168>
>
> WARNING: There is a bond of 6.357250 angstroms between:
>
> ------- .R<GRA 2>.A<C138 165> and .R<GRA 2>.A<C139 166>
>
> WARNING: There is a bond of 8.336572 angstroms between:
>
> ------- .R<GRA 2>.A<C137 163> and .R<GRA 2>.A<C138 165>
>
> WARNING: There is a bond of 6.369506 angstroms between:
>
> ------- .R<GRA 3>.A<C138 165> and .R<GRA 3>.A<C140 168>
>
> WARNING: There is a bond of 6.359170 angstroms between:
>
> ------- .R<GRA 3>.A<C138 165> and .R<GRA 3>.A<C139 166>
>
> WARNING: There is a bond of 9.346460 angstroms between:
>
> ------- .R<GRA 3>.A<C137 163> and .R<GRA 3>.A<H6 164>
>
> WARNING: There is a bond of 9.828253 angstroms between:
>
> ------- .R<GRA 3>.A<C126 162> and .R<GRA 3>.A<C137 163>
>
> WARNING: There is a bond of 11.735002 angstroms between:
>
> ------- .R<GRA 3>.A<C131 97> and .R<GRA 3>.A<H1 98>
>
> WARNING: There is a bond of 9.590395 angstroms between:
>
> ------- .R<GRA 3>.A<C131 97> and .R<GRA 3>.A<C132 99>
>
> WARNING: There is a bond of 11.027230 angstroms between:
>
> ------- .R<GRA 3>.A<C130 95> and .R<GRA 3>.A<C131 97>
>
> WARNING: There is a bond of 6.372918 angstroms between:
>
> ------- .R<GRA 4>.A<C138 165> and .R<GRA 4>.A<C140 168>
>
> WARNING: There is a bond of 6.359739 angstroms between:
>
> ------- .R<GRA 4>.A<C138 165> and .R<GRA 4>.A<C139 166>
>
> WARNING: There is a bond of 8.339672 angstroms between:
>
> ------- .R<GRA 4>.A<C137 163> and .R<GRA 4>.A<C138 165>
>
>
> -- ignoring the warnings.
>
>
> Building topology.
>
> Building atom parameters.
>
> Building bond parameters.
>
> Building angle parameters.
>
> Building proper torsion parameters.
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-cc-ca-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-cc-ca-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-cc-ca-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for ha-c2-cc-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> ** No torsion terms for ha-cc-ca-ca
>
> ** No torsion terms for c2-cc-ca-ca
>
> ** No torsion terms for ca-ca-cc-c2
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for ca-cc-c2-ha
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-ca-ca
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for cc-cc-c2-ha
>
> ** No torsion terms for ca-ca-cc-ha
>
> ** No torsion terms for ca-ca-cc-cc
>
> Building improper torsion parameters.
>
> total 282 improper torsions applied
>
> Building H-Bond parameters.
>
> Parameter file was not saved.
>
> Apparently I have "**No torsion terms for" multiple bonds. I looked and
> apparently I can manually input these torsion angles but I don't know where
> to find them after much time of looking. Could someone help me in fixing
> this issue.
>
> Thanks
> Shalton Evans
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 16 Mar 2015 08:15:03 +0100
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] [q4md-fft] Modify RNA's sugar and adding partial
> charges
> To: q4md-fft.q4md-forcefieldtools.org
> Cc: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150316081503.z31vqnwb6s8wows4.webmail.u-picardie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Jacob,
>
> > In addition to that, I would like to mention that I have posted my
> question
> > on amber mailing list. May be they can give me some alternative which I
> can
> > do easily.
>
> We have implemented the Amber approach developed by Cieplak et al. in
> PyRED...
>
> > I am still strugling with my problem as I couldn't understand much from
> the
> > tutorial you suggested me as I am very new to computational field. Hope I
> > will get it soon:-)
>
> To understand load an Amber force field in LEaP:
>
> xleap -f leaprc.ff99SB (or whatever new version)
> edit DC # to visualize the structure
> edit DC3
> edit DC5
>
> > charge DC # to display the total charge
> Total unperturbed charge: -1.000000
> Total perturbed charge: -1.000000
> > charge DC3
> Total unperturbed charge: -0.692100
> Total perturbed charge: -0.692100
> > charge DC5
> Total unperturbed charge: -0.307900
> Total perturbed charge: -0.307900
>
> -0.6921 + -0.3079 = -1.0000
> charge (DC3 + DC5) = charge DC; idem for A, C, G, U
>
> You can see that to construct an oligonucleotide you need for each
> nucleoside three fragments: the 5'-terminal, the central and the
> 3'-terminal ones...
>
> TTT = sequence { DC5 DC DC3 }
> charge TTT
>
> To construct these 3 fragments, you need to start from a nucleo_SIDE_
> and dimethylphosphate:
> See http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
> & http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
>
> and force the charges of some groups of atoms to take some values to
> be compatible with Amber values; i.e. use inter-molecular charge
> constraints during the charge fitting step; then PyRED does the job,
> generate the FF libs, the FF parameters as well as a LEaP script...
>
> Create a nucleoside for your modified nucleoside & try:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#28
>
> See
>
> http://q4md-forcefieldtools.org/Tutorial/PyRED/All-frag-Nuc/listing-2mol.pdf
> to try to not be lost by the files generated by PyRED ;-)
>
> Run a PyRED job, then request for help if needed; see:
> http://q4md-forcefieldtools.org/REDServer-Development/faq.php#5
> When describing the problem you encountered with R.E.D. Server
> Development, please also provide the 'PXXXX' R.E.D. Server Development
> job name in the body of your email so that we can more easily assist
> you.
>
> I hope this helps...
>
> regards, Francois
>
>
> > On Mar 14, 2015 6:49 PM, "FyD" <fyd.q4md-forcefieldtools.org> wrote:
> >
> >> Dear Jacob,
> >>
> >> I have downloaded a RNA molecule pdb from Nucleic acid databse. When I
> am
> >>> trying to modify its sugar ring ( as I want to cleave its c2' - c3'
> bond),
> >>> loading it again in leap (AMBER) giving me the unmodified structure.
> >>> Please
> >>> suggest how can I modify all sugar ring present in the RNA and how to
> add
> >>> partial charges to the modified residues for MD simulations.
> >>>
> >>
> >> You need to generate the different fragments:
> >> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#27
> >>
> >> PyRED will generate a leaprc.cmd file that can be adapted to be directly
> >> used in LEaP.
> >>
> >> "loading it again in leap (AMBER) giving me the unmodified structure"...
> >> -> difficult to help without looking at the problem...
> >>
> >> "as I want to cleave its c2' - c3' bond"
> >> -> so you have a non-cyclic molecule.
> >>
> >> in general you first load the FF libraries corresponding to the
> different
> >> required molecular fragments and then you load the PDB file (often the
> >> experimental data) of an oligonucleotide. To get a match between the FF
> >> libs and the PDB file, the residue & name names available in the FF libs
> >> have to match these in the PDB file...
> >>
> >> if the residue/atom names in the PDB file correspond to these of the
> >> natural residues, I am not surprised LEaP tries to match/reconstruct the
> >> natural residues (in particular if atoms are missing in the PDB file).
> >>
> >> regards, Francois
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 16 Mar 2015 15:30:40 +0800 (GMT+08:00)
> From: "Wang Moye" <wangmoye13.mails.ucas.ac.cn>
> Subject: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
> To: amber <amber.ambermd.org>
> Message-ID:
> <1c587b3.1a159.14c217de2e0.Coremail.wangmoye13.mails.ucas.ac.cn>
> Content-Type: text/plain; charset=GBK
>
>
> Hello everyone!
> I am a new user.There is a question in my objection and I need your help.
> I run a REMD process in AMBER12.Now I obtain some output files.Like this:
> remd.mdcrd.001
> remd.mdcrd.002
> ...remd.mdcrd.026
> and remd.mdinfo.001.. remd.mdinfo.026
> and remd.rst.001.. remd.rst.002
> and remd.mdout.001.. remd.mdout.026
> Total 26 replicas. I want to get the 3D free energy surface picture about
> my protein. Two coordinates are respectively Rg and RMSD.
> Someone told me the WHAM code can do this. I have the WHAM code now, but I
> don't know how to use the WHAM to deal with my AMBER's output files to
> obtain the metafile. Should I write the Rg and RMSD information into a
> single metafile? How to achieve this using the outputfile above? Need I
> write some scripts to get the value of Rg and RMSD?
> If you know how to deal with it, please help me. Thank you very much!
>
>
> --
> Wang moye
>
> University of Chinese Academy of Sciences
>
> 2015/3
>
>
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 16 Mar 2015 15:29:06 +0530
> From: Sohag Biswas <cy13p1001.iith.ac.in>
> Subject: [AMBER] facing problem to create a prmtop file for oxonium
> cation
> To: amber.ambermd.org
> Message-ID:
> <CAJNMk+bfZvbJ1SWZ1QuiM8wZ8sUtwUM=nxjX6=
> zF2tEgDFJW1w.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear amaber users,
>
> In attempt to create a topology file for oxonium cation from pdb file by
> following command, it is showing,
>
> For atom[1]:O1, the best APS is not zero, bonds involved by this atom are
> frozen
>
> The command line is
>
> antechamber -i eth.pdb -fi pdb -o eth.prepi -fo prepi -c bcc -nc 1 -at gaff
> -pf y
>
> It will be very helpful for helping me. Many Many thanks to all. Here i am
> attaching also the pdb file which i created by xleap.
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: eth.pdb
> Type: chemical/x-pdb
> Size: 1481 bytes
> Desc: not available
> Url :
> http://lists.ambermd.org/mailman/private/amber/attachments/20150316/f651a5c0/attachment-0001.pdb
>
> ------------------------------
>
> Message: 10
> Date: Mon, 16 Mar 2015 11:06:47 +0100
> From: Jennifer Vo <quyviolet.gmail.com>
> Subject: [AMBER] diisopropylethylene parameter
> To: amber.ambermd.org
> Message-ID:
> <
> CAD+ki7gfT6atBVxOASAcxWcbL4TD3T7fK96Y+VEr2YSLncje4A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
>
> Does anyone has the itp file for diisopropylethylene? It would be very
> helpful if you can share.
> Many thanks in advance.
> Regards,
> Jennifer
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 16 Mar 2015 18:18:03 +0800
> From: Vijay Achari <glycoamber.gmail.com>
> Subject: Re: [AMBER] finding angles
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CA+-itZjbSM-KNfKTq2exOt1gEFtuCqj4qN9w2Yu6WJJGrSc4fg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> There was a space after "z", as below:
> [vector v1 principal z ]
>
> This should be
>
> [vector v1 principal z]
>
> Regards
>
>
>
>
>
> On Fri, Mar 13, 2015 at 11:40 AM, Vijay Achari <glycoamber.gmail.com>
> wrote:
>
> > OK,
> >
> > Let me update the cpptraj and test it again.
> > Vj
> >
> > On Fri, Mar 13, 2015 at 11:15 AM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> >> On Thu, Mar 12, 2015 at 7:24 PM, Vijay Achari <glycoamber.gmail.com>
> >> wrote:
> >> > [vector v1 principal z ]
> >> > VECTOR: Type Principal X, mask [*]
> >> > Error: [vector] Not all arguments handled: [ z ]
> >>
> >> That's weird - when I run the same command I get:
> >>
> >> > vector v1 principal z
> >> VECTOR: Type Principal Z, mask [*]
> >>
> >> I notice that your CPPTRAJ is a bit out of date. Try updating to the
> >> latest version (14.25) and see if that helps. Also make sure all of
> >> your cpptraj test cases are passing.
> >>
> >> -Dan
> >>
> >> > 1 errors encountered reading input.
> >> > TIME: Total execution time: 0.0568 seconds.
> >> >
> >> > vijay.micelle
> >>
> :~/Simulation/chapter6-lyo-paper3-Vj/lyo-Analysis2/struc-10-tail-to-Z-angle-distribution/Chain-Angle-distribution-betaLyo25perR$
> >> >
> >> >
> >> > Thank you.
> >> >
> >> > On Thu, Mar 12, 2015 at 11:20 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >
> >> >> Hi,
> >> >>
> >> >> On Thu, Mar 12, 2015 at 8:00 AM, Vijay Achari <glycoamber.gmail.com>
> >> >> wrote:
> >> >> > *vector v1 principal z vector v2 :1.C50 :1.C80vectormath vec1
> v1
> >> >> vec2
> >> >> > v2 out vectorTimesdat name chainAngle dotangle*
> >> >> > But I get error.
> >> >>
> >> >> Your input is mangled - seems like your newlines are not making it to
> >> >> your email. Make sure you're sending everything in plain text mode.
> >> >> Also, don't just say you got an "error" - actually report the *exact*
> >> >> error message, otherwise our chances of effectively helping you are
> >> >> slim.
> >> >>
> >> >> -Dan
> >> >>
> >> >> --
> >> >> -------------------------
> >> >> Daniel R. Roe, PhD
> >> >> Department of Medicinal Chemistry
> >> >> University of Utah
> >> >> 30 South 2000 East, Room 307
> >> >> Salt Lake City, UT 84112-5820
> >> >> http://home.chpc.utah.edu/~cheatham/
> >> >> (801) 587-9652
> >> >> (801) 585-6208 (Fax)
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 16 Mar 2015 10:32:25 +0000
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] facing problem to create a prmtop file for
> oxonium cation
> To: <amber.ambermd.org>
> Message-ID: <20150316103225.1affb50e.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> I would think a (trialkyl) oxonium is outside the range of molecules
> antechamber was designed for. You should probably also check if a AM1
> Hamiltonian (used in the bcc charge method) is really appropriate for
> your molecule.
>
> On Mon, 16 Mar 2015 15:29:06 +0530
> Sohag Biswas <cy13p1001.iith.ac.in> wrote:
>
> > Dear amaber users,
> >
> > In attempt to create a topology file for oxonium cation from pdb file
> > by following command, it is showing,
> >
> > For atom[1]:O1, the best APS is not zero, bonds involved by this atom
> > are frozen
> >
> > The command line is
> >
> > antechamber -i eth.pdb -fi pdb -o eth.prepi -fo prepi -c bcc -nc 1
> > -at gaff -pf y
> >
> > It will be very helpful for helping me. Many Many thanks to all. Here
> > i am attaching also the pdb file which i created by xleap.
>
>
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 16 Mar 2015 10:37:41 +0000
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] diisopropylethylene parameter
> To: <amber.ambermd.org>
> Message-ID: <20150316103741.6cb3b288.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> ITP is the include topology file for GROMACS so this may be not the
> right forum to ask this. What you probably want is to have force field
> parameters for this molecule but you don't say which one you plan to
> use. In any case, I would suggest to scan the literature if you do
> not want to do parameterise yourself. Also, the trivial name suggests
> to me that these are (at least) three different molecules.
>
> On Mon, 16 Mar 2015 11:06:47 +0100
> Jennifer Vo <quyviolet.gmail.com> wrote:
>
> > Dear All,
> >
> > Does anyone has the itp file for diisopropylethylene? It would be very
> > helpful if you can share.
> > Many thanks in advance.
> > Regards,
> > Jennifer
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 16 Mar 2015 07:47:41 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] facing problem to create a prmtop file for
> oxonium cation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150316114741.GB43801.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Mar 16, 2015, Sohag Biswas wrote:
> >
> > In attempt to create a topology file for oxonium cation from pdb file by
> > following command, it is showing,
> >
> > For atom[1]:O1, the best APS is not zero, bonds involved by this atom are
> > frozen
>
> To add to what Hannes said: the message above is just for information, and
> is
> not an error.
>
> As with all antechamber output, you should treat the resulting force field
> with care: it is often just a first pass. In this case, look carefully at
> the
> atom types and parameters associated with atom O1.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 15
> Date: Mon, 16 Mar 2015 08:19:18 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Using WHAM to get 3D free energy surface in
> AMBER12
> To: amber.ambermd.org
> Message-ID: <1426508358.12272.4.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2015-03-16 at 15:30 +0800, Wang Moye wrote:
> > Hello everyone!
> > I am a new user.There is a question in my objection and I need your
> > help. I run a REMD process in AMBER12.Now I obtain some output
> > files.Like this:
> > remd.mdcrd.001
> > remd.mdcrd.002
> > ...remd.mdcrd.026
> > and remd.mdinfo.001.. remd.mdinfo.026
> > and remd.rst.001.. remd.rst.002
> > and remd.mdout.001.. remd.mdout.026
> > Total 26 replicas. I want to get the 3D free energy surface picture
> > about my protein. Two coordinates are respectively Rg and RMSD.
> > Someone told me the WHAM code can do this. I have the WHAM code now,
> > but I don't know how to use the WHAM to deal with my AMBER's output
> > files to obtain the metafile. Should I write the Rg and RMSD
> > information into a single metafile? How to achieve this using the
> > outputfile above? Need I write some scripts to get the value of Rg
> > and RMSD?
> > If you know how to deal with it, please help me. Thank you very much!
>
> What kind of REMD did you do? Umbrella-REMD? Temperature-REMD?
> pH-REMD?
>
> Also, WHAM is a method, not a program. There are programs that
> implement WHAM, like the one from Grossfield's lab (I think that's the
> one you're talking about?)
>
> If you did not use biased sampling (like umbrella sampling), then you
> don't need a weighted histogram method -- just do unbiased histogramming
> and calculate your free energy from that.
>
> If you *did* do biased sampling, then there is an example constructing
> the WHAM metafile for Grossfield's program here:
> http://ambermd.org/tutorials/advanced/tutorial17/ (specifically section
> 3: http://ambermd.org/tutorials/advanced/tutorial17/section3.htm).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 16 Mar 2015 13:31:01 +0100
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] facing problem to create a prmtop file for
> oxonium cation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150316133101.6x3w780ysk0cw4sk.webmail.u-picardie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Sohag,
>
> You could use R.E.D. Server Dev./PyRED at:
> http://q4md-forcefieldtools.org/REDServer-Development/
>
> You can easily run a test providing the PDB input file (with a total
> charge = +1 in columns 79/80 of that PDB file for that O+ atom).
>
> You can let PyRED do the job automatically or provide your own options:
> - different theory levels for QM computations
> - provide your own FF parameters using the frcmod.user file
> - provide your own atom types; see MOLECULE1-ATMTYPE
> etc...
> See http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
>
> regards, Francois
>
>
> > In attempt to create a topology file for oxonium cation from pdb file by
> > following command, it is showing,
> >
> > For atom[1]:O1, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > The command line is
> > antechamber -i eth.pdb -fi pdb -o eth.prepi -fo prepi -c bcc -nc 1 -at
> gaff
> > -pf y
> >
> > It will be very helpful for helping me. Many Many thanks to all. Here i
> am
> > attaching also the pdb file which i created by xleap.
>
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Mon, 16 Mar 2015 14:00:19 +0100
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] Decomposition of the MMGBSA based on multi
> trajectory input
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopzSQ=
> Kb06jwW-mxQWhrt55Xugp1VARkFtLFzKZw1E4s0A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Bill,
>
> just faced with the error of the post-processing of such trajectories
> and topologiest
>
> 1) here I'm using ante-MMPBSA.py just to create three input topologies
> for mmgbsa.py providing already stripped topology (only protein and
> ligand).
>
> ante-MMPBSA.py -p ${sim}/strip.protein.parm7 -c complex.prmtop -r
> receptor.prmtop -l ligand.prmtop -n :MOL
>
>
> 2) then I use three generated prmtops (here I checked it according to
> the number of atoms in each- all should be correct for first instance)
> as well as 2 stripped trajectories as the inputs for the mmgbsa:
> nmpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
> mmgbsa_nm_${simulation}.dat -sp ${sim}/strip.protein.parm7 -cp
> ${sim}/strip.protein.parm7 -rp receptor.prmtop -y
> ${sim}/merged_md1_2.nc ${sim}/striped_md3.nc -lp ligand.prmtop >
> progress.log 2>&1" > ./mmgbsa_${simulation}.pbs
>
> 3) having input file for the decomposition
>
> &general
> startframe= 1, interval=50, keep_files=2, netcdf=1
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &decomp
> idecomp=1, csv_format=0, dec_verbose=0,
>
>
> the calculation is begining- so there is no problems with any of
> inputs- but occasionally I've obtained error
>
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13
> CalcError: /home/cmoon/Prog/amber12/bin/cpptraj failed with prmtop
> /home/cmoon/total_decomp/5p3_carvone/strip.protein.parm7!
> Error occured on rank 14.
>
> How it could be fixed most trivially?
>
>
> James
>
> 2015-03-05 13:44 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
> > Personally, I use tleap to generate all prmtops necessary for MMPBSA.py
> calculations prior to running any simulation. But if you have already
> started running simulations, I would advise using ante-MMPBSA.py
> >
> > -Bill
> >
> > On Mar 5, 2015, at 6:39 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> >
> >> so in simplest case only 2 inputs should be provided : stripped
> >> merged trajectory as well as stripped topology for each system
> >> shouldn't it? BTW is it possible to use ante-mmpbsa to strip common
> >> mask from several input trajectories consisted of different number of
> >> solvent (so its number of atoms will be also different) or it will
> >> better anyway to use tleap?
> >>
> >> James
> >>
> >> 2015-03-05 11:45 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> >>> Thanks alot!
> >>>
> >>> James
> >>>
> >>> 2015-03-04 16:38 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
> >>>> For MMPBSA.py calculations, explicit solvent molecules are never used
> for
> >>>> the calculation. MMPBSA.py removes the solvent before doing any
> >>>> calculations. So if you give it a trajectory (or multiple
> trajectories)
> >>>> without water molecules along with a dry/stripped topology, the
> calculation
> >>>> will be the same, but MMPBSA.py just won't have to remove the water
> atoms
> >>>> first.
> >>>>
> >>>> In this case, you do not need to specify anything for the strip mask.
> If
> >>>> you don't give MMPBSA.py a solvated topology file, it knows not to
> strip
> >>>> any residues from the trajectory.
> >>>>
> >>>> You can use the startframe variable in the &general namelist to
> specify
> >>>> what frame you want the calculation to start on. And I believe that
> is for
> >>>> each trajectory if you provide more than one.
> >>>>
> >>>> -Bill
> >>>>
> >>>> On Wed, Mar 4, 2015 at 9:48 AM, James Starlight <
> jmsstarlight.gmail.com>
> >>>> wrote:
> >>>>
> >>>>> and some additional questions:
> >>>>>
> >>>>> 1- what should be provided in the mmgbsa.input file for the stripped
> >>>>> mask in case when I use already stripped from the solvent
> trajectories
> >>>>> 2- how it possible not to take into the analysis x fist snapshots
> from
> >>>>> each processed trajectory used within one mmgbsa calculation?
> >>>>>
> >>>>> James
> >>>>>
> >>>>> 2015-03-04 15:10 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> >>>>>> Hi Bill,
> >>>>>>
> >>>>>> so I'd like to specify more:
> >>>>>> mmgbsa.py accept *several* input trajectories files (specified
> after
> >>>>>> its -y flag) each of which should consist only of the atoms for
> ligand
> >>>>>> and receptor as well as stripped topology with the same atoms isn't
> >>>>>> it? so for calculation of the free energy of binding and its
> >>>>>> decomposition the presence of solvent within the system is not
> needed?
> >>>>>>
> >>>>>> Regards,
> >>>>>>
> >>>>>> James
> >>>>>>
> >>>>>> 2015-03-03 16:23 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
> >>>>>>> You will need to strip all the water molecules out of the
> trajectories
> >>>>>>> using cpptraj prior to running MMPBSA.py since they all have
> different
> >>>>>>> numbers of water molecules, and then use the dry prmtop and just
> don't
> >>>>>>> provide a solvated prmtop. You don't have to merge them all into
> one
> >>>>>>> trajectory using cpptraj prior to running MMPBSA.py. You can just
> use a
> >>>>>>> wild card or just list them all after the -y flag in the MMPBSA.py
> >>>>> command.
> >>>>>>>
> >>>>>>> I hope that helps.
> >>>>>>>
> >>>>>>> -Bill
> >>>>>>>
> >>>>>>> On Tue, Mar 3, 2015 at 6:58 AM, James Starlight <
> jmsstarlight.gmail.com
> >>>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>>> Dear Amber users!
> >>>>>>>>
> >>>>>>>> I'm going to perform per-residue decomposition analysis for
> several
> >>>>>>>> protein-ligand systems having 3 independent trajectories for each
> >>>>>>>> system. I wounded to know
> >>>>>>>> 1) is it possible to include several trajectories tax the standard
> >>>>>>>> input to MMPBSA.py or alternatively I should to merge all
> trajectories
> >>>>>>>> for the same system together using cpptraj?
> >>>>>>>> 2) what I should do if some of the trajectories for the same
> system
> >>>>>>>> are consisted of different number of atoms (and its parm7 files
> also
> >>>>>>>> differs)-> because each time each system has been solvated de
> novo->
> >>>>>>>> so the number of solvent molecules in identical protein-ligand
> systems
> >>>>>>>> are differs. In these regards Is it possible to i) strip all
> solvent
> >>>>>>>> using cpptraj from each trajectory and ii) to join all of them
> >>>>>>>> together ( consisted of only protein-ligand atoms) iii) to provide
> >>>>>>>> stripped parm7 file for the MMPBSA.py as well as the stripped
> >>>>>>>> trajectory.
> >>>>>>>>
> >>>>>>>> I would be very thankful for any other solutions,
> >>>>>>>>
> >>>>>>>> James
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER mailing list
> >>>>>>>> AMBER.ambermd.org
> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Bill Miller III
> >>>>>>> Post-doc
> >>>>>>> University of Richmond
> >>>>>>> 417-549-0952
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Bill Miller III
> >>>> Post-doc
> >>>> University of Richmond
> >>>> 417-549-0952
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 18
> Date: Mon, 16 Mar 2015 14:42:16 +0100
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] Decomposition of the MMGBSA based on multi
> trajectory input
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopwr7pchRiiY=ZnE+Z1Mq2pK0OguSFRm2S=
> XA8aauefmqw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> some update:
> I've noticed that the above error takes place when I used both
> trajectories provided in the -y for the mmgbsa (here the second
> trajectory has been stripped from different system initially consisted
> of different number solvent molecules. However both stripped
> topologies (obtained for each trajectories) consists of the same
> number of atoms so I have no idea why such error take place.
>
> James
>
> 2015-03-16 14:00 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> > Hi Bill,
> >
> > just faced with the error of the post-processing of such trajectories
> > and topologiest
> >
> > 1) here I'm using ante-MMPBSA.py just to create three input topologies
> > for mmgbsa.py providing already stripped topology (only protein and
> > ligand).
> >
> > ante-MMPBSA.py -p ${sim}/strip.protein.parm7 -c complex.prmtop -r
> > receptor.prmtop -l ligand.prmtop -n :MOL
> >
> >
> > 2) then I use three generated prmtops (here I checked it according to
> > the number of atoms in each- all should be correct for first instance)
> > as well as 2 stripped trajectories as the inputs for the mmgbsa:
> > nmpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
> > mmgbsa_nm_${simulation}.dat -sp ${sim}/strip.protein.parm7 -cp
> > ${sim}/strip.protein.parm7 -rp receptor.prmtop -y
> > ${sim}/merged_md1_2.nc ${sim}/striped_md3.nc -lp ligand.prmtop >
> > progress.log 2>&1" > ./mmgbsa_${simulation}.pbs
> >
> > 3) having input file for the decomposition
> >
> > &general
> > startframe= 1, interval=50, keep_files=2, netcdf=1
> > /
> > &gb
> > igb=5, saltcon=0.150,
> > /
> > &decomp
> > idecomp=1, csv_format=0, dec_verbose=0,
> >
> >
> > the calculation is begining- so there is no problems with any of
> > inputs- but occasionally I've obtained error
> >
> > Exiting. All files have been retained.
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13
> > CalcError: /home/cmoon/Prog/amber12/bin/cpptraj failed with prmtop
> > /home/cmoon/total_decomp/5p3_carvone/strip.protein.parm7!
> > Error occured on rank 14.
> >
> > How it could be fixed most trivially?
> >
> >
> > James
> >
> > 2015-03-05 13:44 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
> >> Personally, I use tleap to generate all prmtops necessary for MMPBSA.py
> calculations prior to running any simulation. But if you have already
> started running simulations, I would advise using ante-MMPBSA.py
> >>
> >> -Bill
> >>
> >> On Mar 5, 2015, at 6:39 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> >>
> >>> so in simplest case only 2 inputs should be provided : stripped
> >>> merged trajectory as well as stripped topology for each system
> >>> shouldn't it? BTW is it possible to use ante-mmpbsa to strip common
> >>> mask from several input trajectories consisted of different number of
> >>> solvent (so its number of atoms will be also different) or it will
> >>> better anyway to use tleap?
> >>>
> >>> James
> >>>
> >>> 2015-03-05 11:45 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> >>>> Thanks alot!
> >>>>
> >>>> James
> >>>>
> >>>> 2015-03-04 16:38 GMT+01:00 Bill Miller III <brmilleriii.gmail.com>:
> >>>>> For MMPBSA.py calculations, explicit solvent molecules are never
> used for
> >>>>> the calculation. MMPBSA.py removes the solvent before doing any
> >>>>> calculations. So if you give it a trajectory (or multiple
> trajectories)
> >>>>> without water molecules along with a dry/stripped topology, the
> calculation
> >>>>> will be the same, but MMPBSA.py just won't have to remove the water
> atoms
> >>>>> first.
> >>>>>
> >>>>> In this case, you do not need to specify anything for the strip
> mask. If
> >>>>> you don't give MMPBSA.py a solvated topology file, it knows not to
> strip
> >>>>> any residues from the trajectory.
> >>>>>
> >>>>> You can use the startframe variable in the &general namelist to
> specify
> >>>>> what frame you want the calculation to start on. And I believe that
> is for
> >>>>> each trajectory if you provide more than one.
> >>>>>
> >>>>> -Bill
> >>>>>
> >>>>> On Wed, Mar 4, 2015 at 9:48 AM, James Starlight <
> jmsstarlight.gmail.com>
> >>>>> wrote:
> >>>>>
> >>>>>> and some additional questions:
> >>>>>>
> >>>>>> 1- what should be provided in the mmgbsa.input file for the stripped
> >>>>>> mask in case when I use already stripped from the solvent
> trajectories
> >>>>>> 2- how it possible not to take into the analysis x fist snapshots
> from
> >>>>>> each processed trajectory used within one mmgbsa calculation?
> >>>>>>
> >>>>>> James
> >>>>>>
> >>>>>> 2015-03-04 15:10 GMT+01:00 James Starlight <jmsstarlight.gmail.com
> >:
> >>>>>>> Hi Bill,
> >>>>>>>
> >>>>>>> so I'd like to specify more:
> >>>>>>> mmgbsa.py accept *several* input trajectories files (specified
> after
> >>>>>>> its -y flag) each of which should consist only of the atoms for
> ligand
> >>>>>>> and receptor as well as stripped topology with the same atoms isn't
> >>>>>>> it? so for calculation of the free energy of binding and its
> >>>>>>> decomposition the presence of solvent within the system is not
> needed?
> >>>>>>>
> >>>>>>> Regards,
> >>>>>>>
> >>>>>>> James
> >>>>>>>
> >>>>>>> 2015-03-03 16:23 GMT+01:00 Bill Miller III <brmilleriii.gmail.com
> >:
> >>>>>>>> You will need to strip all the water molecules out of the
> trajectories
> >>>>>>>> using cpptraj prior to running MMPBSA.py since they all have
> different
> >>>>>>>> numbers of water molecules, and then use the dry prmtop and just
> don't
> >>>>>>>> provide a solvated prmtop. You don't have to merge them all into
> one
> >>>>>>>> trajectory using cpptraj prior to running MMPBSA.py. You can just
> use a
> >>>>>>>> wild card or just list them all after the -y flag in the MMPBSA.py
> >>>>>> command.
> >>>>>>>>
> >>>>>>>> I hope that helps.
> >>>>>>>>
> >>>>>>>> -Bill
> >>>>>>>>
> >>>>>>>> On Tue, Mar 3, 2015 at 6:58 AM, James Starlight <
> jmsstarlight.gmail.com
> >>>>>>>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> Dear Amber users!
> >>>>>>>>>
> >>>>>>>>> I'm going to perform per-residue decomposition analysis for
> several
> >>>>>>>>> protein-ligand systems having 3 independent trajectories for each
> >>>>>>>>> system. I wounded to know
> >>>>>>>>> 1) is it possible to include several trajectories tax the
> standard
> >>>>>>>>> input to MMPBSA.py or alternatively I should to merge all
> trajectories
> >>>>>>>>> for the same system together using cpptraj?
> >>>>>>>>> 2) what I should do if some of the trajectories for the same
> system
> >>>>>>>>> are consisted of different number of atoms (and its parm7 files
> also
> >>>>>>>>> differs)-> because each time each system has been solvated de
> novo->
> >>>>>>>>> so the number of solvent molecules in identical protein-ligand
> systems
> >>>>>>>>> are differs. In these regards Is it possible to i) strip all
> solvent
> >>>>>>>>> using cpptraj from each trajectory and ii) to join all of them
> >>>>>>>>> together ( consisted of only protein-ligand atoms) iii) to
> provide
> >>>>>>>>> stripped parm7 file for the MMPBSA.py as well as the stripped
> >>>>>>>>> trajectory.
> >>>>>>>>>
> >>>>>>>>> I would be very thankful for any other solutions,
> >>>>>>>>>
> >>>>>>>>> James
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> AMBER mailing list
> >>>>>>>>> AMBER.ambermd.org
> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> Bill Miller III
> >>>>>>>> Post-doc
> >>>>>>>> University of Richmond
> >>>>>>>> 417-549-0952
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER mailing list
> >>>>>>>> AMBER.ambermd.org
> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Bill Miller III
> >>>>> Post-doc
> >>>>> University of Richmond
> >>>>> 417-549-0952
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 19
> Date: Mon, 16 Mar 2015 09:45:47 -0400
> From: Lara rajam <lara.4884.gmail.com>
> Subject: [AMBER] organic molecule
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPQ+66DV-Fx=
> xCC9wSSHEfwGATQ6PRu5sFr8jqXZJCuoy-UnEg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber !
>
> If one want to perform a small molecule (organic molecule ) dynamics in
> water.
> Is it possible to do in AMBER.
> I would like to know some reference paper if there is any .
> thank you
>
>
> ------------------------------
>
> Message: 20
> Date: Mon, 16 Mar 2015 21:49:12 +0800
> From: maryam azimzadehirani <maryamai1988.gmail.com>
> Subject: [AMBER] Per-residue decomposition energy MMGBSA.py
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEVOLfqJUbwxxiExXJThn82reBx_GYuchXL5x6fX9xqnUdO-qg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
> Can anyone simply explains to me how MMGBSA.py calculates per-residue
> decomposition energy?
> I assume it is similar to binding energy calculation where it calculates
> the free energy of ligand (solvated and in vacuum), free energy of receptor
> (solvated and in vacuum) and ligand-receptor free energy (solvated and in
> vacuum). Then calculate Gibbs free energy of binding, as they mentioned in
> advance tutorial 3:
>
>
>
> If we don't talk about entropy at all, which makes everything confusing...
> In a simple way, the same method is used for each residue in per-residue
> decomposition calculation, where the whole ligand is replaced by each
> residue that we chose in the mask?
> Please correct me if I am wrong.
> Regards,
> Maryam
>
>
> ------------------------------
>
> Message: 21
> Date: Mon, 16 Mar 2015 07:58:33 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] finding angles
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAAC0qOawtg1+iVCPWCJSV9vgSMDJ00JHNNs+M1ONPtkoFZxPxw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> That shouldn't happen since cpptraj removes whitespace from input commands.
> Are you enclosing your input commands in quotes or something?
>
> -Dan
>
> On Monday, March 16, 2015, Vijay Achari <glycoamber.gmail.com> wrote:
>
> > There was a space after "z", as below:
> > [vector v1 principal z ]
> >
> > This should be
> >
> > [vector v1 principal z]
> >
> > Regards
> >
> >
> >
> >
> >
> > On Fri, Mar 13, 2015 at 11:40 AM, Vijay Achari <glycoamber.gmail.com
> > <javascript:;>> wrote:
> >
> > > OK,
> > >
> > > Let me update the cpptraj and test it again.
> > > Vj
> > >
> > > On Fri, Mar 13, 2015 at 11:15 AM, Daniel Roe <daniel.r.roe.gmail.com
> > <javascript:;>>
> > > wrote:
> > >
> > >> On Thu, Mar 12, 2015 at 7:24 PM, Vijay Achari <glycoamber.gmail.com
> > <javascript:;>>
> > >> wrote:
> > >> > [vector v1 principal z ]
> > >> > VECTOR: Type Principal X, mask [*]
> > >> > Error: [vector] Not all arguments handled: [ z ]
> > >>
> > >> That's weird - when I run the same command I get:
> > >>
> > >> > vector v1 principal z
> > >> VECTOR: Type Principal Z, mask [*]
> > >>
> > >> I notice that your CPPTRAJ is a bit out of date. Try updating to the
> > >> latest version (14.25) and see if that helps. Also make sure all of
> > >> your cpptraj test cases are passing.
> > >>
> > >> -Dan
> > >>
> > >> > 1 errors encountered reading input.
> > >> > TIME: Total execution time: 0.0568 seconds.
> > >> >
> > >> > vijay.micelle
> > >>
> >
> :~/Simulation/chapter6-lyo-paper3-Vj/lyo-Analysis2/struc-10-tail-to-Z-angle-distribution/Chain-Angle-distribution-betaLyo25perR$
> > >> >
> > >> >
> > >> > Thank you.
> > >> >
> > >> > On Thu, Mar 12, 2015 at 11:20 PM, Daniel Roe <
> daniel.r.roe.gmail.com
> > <javascript:;>>
> > >> wrote:
> > >> >
> > >> >> Hi,
> > >> >>
> > >> >> On Thu, Mar 12, 2015 at 8:00 AM, Vijay Achari <
> glycoamber.gmail.com
> > <javascript:;>>
> > >> >> wrote:
> > >> >> > *vector v1 principal z vector v2 :1.C50 :1.C80vectormath vec1
> > v1
> > >> >> vec2
> > >> >> > v2 out vectorTimesdat name chainAngle dotangle*
> > >> >> > But I get error.
> > >> >>
> > >> >> Your input is mangled - seems like your newlines are not making it
> to
> > >> >> your email. Make sure you're sending everything in plain text mode.
> > >> >> Also, don't just say you got an "error" - actually report the
> *exact*
> > >> >> error message, otherwise our chances of effectively helping you are
> > >> >> slim.
> > >> >>
> > >> >> -Dan
> > >> >>
> > >> >> --
> > >> >> -------------------------
> > >> >> Daniel R. Roe, PhD
> > >> >> Department of Medicinal Chemistry
> > >> >> University of Utah
> > >> >> 30 South 2000 East, Room 307
> > >> >> Salt Lake City, UT 84112-5820
> > >> >> http://home.chpc.utah.edu/~cheatham/
> > >> >> (801) 587-9652
> > >> >> (801) 585-6208 (Fax)
> > >> >>
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org <javascript:;>
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org <javascript:;>
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe, PhD
> > >> Department of Medicinal Chemistry
> > >> University of Utah
> > >> 30 South 2000 East, Room 307
> > >> Salt Lake City, UT 84112-5820
> > >> http://home.chpc.utah.edu/~cheatham/
> > >> (801) 587-9652
> > >> (801) 585-6208 (Fax)
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org <javascript:;>
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
> ------------------------------
>
> Message: 22
> Date: Mon, 16 Mar 2015 10:15:59 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] organic molecule
> To: amber.ambermd.org
> Message-ID: <1426515359.12272.6.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2015-03-16 at 09:45 -0400, Lara rajam wrote:
> > Dear Amber !
> >
> > If one want to perform a small molecule (organic molecule ) dynamics in
> > water.
> > Is it possible to do in AMBER.
>
> Yes. It's basically the same as doing a regular protein with a bound
> ligand in water. Generate the mol2 and frcmod files for the organic
> molecule using antechamber.
>
> Then load the molecule in tleap and solvate it using "solvateBox" or
> "solvateOct".
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 23
> Date: Mon, 16 Mar 2015 10:26:57 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Per-residue decomposition energy MMGBSA.py
> To: amber.ambermd.org
> Message-ID: <1426516017.12272.17.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2015-03-16 at 21:49 +0800, maryam azimzadehirani wrote:
> > Dear all,
> > Can anyone simply explains to me how MMGBSA.py calculates per-residue
> > decomposition energy?
> > I assume it is similar to binding energy calculation where it calculates
> > the free energy of ligand (solvated and in vacuum), free energy of
> receptor
> > (solvated and in vacuum) and ligand-receptor free energy (solvated and in
> > vacuum). Then calculate Gibbs free energy of binding, as they mentioned
> in
> > advance tutorial 3:
>
> Loosely speaking, this is almost equivalent to what happens.
>
> > If we don't talk about entropy at all, which makes everything
> confusing...
> > In a simple way, the same method is used for each residue in per-residue
> > decomposition calculation, where the whole ligand is replaced by each
> > residue that we chose in the mask?
>
> No, this is not what happens. This would be more "correct" than what is
> currently done (I enclose in quotes since you would need to
> appropriately handle the dangling valences caused by cutting residues
> out of the polymer chain and then account for the extra atoms you needed
> to add to cap that valence... it would be challenging, not to mention
> expensive, to do that "correctly").
>
> What's done in reality for MM/GBSA pairwise decomposition is much
> simpler: the formula for GB free energies is a pairwise sum (see
> equation 4.2 in the Amber 14 manual on page 57, along with Equation
> 4.3). The sum is actually a double-sum (and the 1/2 accounts for
> including both i->j and j->i in the sum).
>
> You can imagine based on this formula calculating the "contribution" to
> the total energy for each atom (or for pairwise decomposition, for each
> atom pair). Then, all you do is add up the energies for each atom in a
> particular residue to get the "per-residue" decomposed energy.
>
> This is rigorously correct if you have a truly pairwise potential energy
> function. While Eq. 4.2 looks that way at first glance, the term R (see
> Eq. 4.5) is itself a sum over all atom pairs as well... which means that
> the GB energy function is *not* pairwise decomposable. But the
> resulting decomposition can be qualitatively useful.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 24
> Date: Tue, 17 Mar 2015 00:50:20 +0800
> From: Vijay Achari <glycoamber.gmail.com>
> Subject: Re: [AMBER] Evaluating hydrogen boding lifetime
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CA+-itZhzPf-pUhqtJJTujRZvO998=
> AMA_koVOKybHrmVBQCmrA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Dan,
>
> Below is the example you gave to explain on how the calculation of HB can
> done with raw data.
>
>
> HB1-1 HB1-2
> 1 0
> 0 1
> 1 0
> 1 1
>
> Using the method I illustrated before you'd come up with an average of
> (5 / 4 = 1.25). However, the actual answer of how often is HB1
> involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
> is broken, HB1-2 is formed, so its always involved in some kind of
> hydrogen bond. So to do what you want you will need to write out the
> raw time series data, sum up the columns corresponding to the hydrogen
> bonds you are interested in, then run 'lifetime' analysis on that data
> set. So using the above sets as an example, the set I would actually
> run lifetime analysis on would look like:
>
>
> Relating to the above example, I understand that we need to add the "1"s
> and divide by total number of lines.
>
> (total of all "1"s) / (total rows with "1"s)
>
>
> So how with the example below? (I modified the above sample).
>
> HB1-1 HB1-2
> 1 0
> 0 1
> 1 0
> 1 1
> 0 1
> 0 0
> 0 0
>
> For the above example is the the average is 6/7 or 6/5. The number 7
> stand for total number of rows and the later stand for rows with the
> presence of "1" (at least once).
>
> Means do I need to count the total rows or the rows with the occurrence of
> "1" only?
>
>
>
> Your explanation would help me to write the script.
>
> Thanks.
>
>
>
> On Thu, Mar 12, 2015 at 4:53 PM, Vijay Achari <glycoamber.gmail.com>
> wrote:
>
> > Dear Dan,
> >
> > Following your explanation, I would like to verify few things.
> >
> > #1) The file that contains the raw data; is this one "solutehb.dat"
> >
> > if yes,
> >
> > #2) The format of the data in the file is as below?
> >
> > #Frame *BMR_42.O22-BMR_1.O23-H23* BMR_49.O13-BMR_1.O13-H13
> > BMR_59.O13-BMR_2.O22-H22 BMR_10.O13-BMR_2.O26-H26 BMR_61.O26-BMR_3
> .O22-H22
> > BMR_23.
> > O25-BMR_4.O12-H12 BMR_23.O26-BMR_4.O13-H13 BMR_23.O25-BMR_4.O13-H13
> > BMR_20.O13-BMR_5.O22-H22 BMR_10.O24-BMR_6.O13-H13 BMR_41.O23-BMR_7
> .O23-H2
> > 3 BMR_41.O24-BMR_7.O23-H23 ....
> >
> >
> > * 1 * 1
> > 1 1 1
> > 1 1 1
> > 1 1 1
> > 1 1 1
> > 1 1 1
> > 1 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1
> > 1 1 1 . . .
> >
> >
> > #3) So need I operate on this file?
> >
> > #4) Is the first data "BMR_42.O22-BMR_1.O23-H23" is corresponding to the
> > value "1" (below #2)
> >
> > Thank you.
> >
> >
> >
> >
> > On Wed, Mar 11, 2015 at 11:11 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> Sorry, it's not clear to me what you're trying to calculate. You said
> >> "I want to know the lifetime of HB for O22 (ACCEPTOR) atom only"; do
> >> you want the average lifetime of any given O22 involved in a hydrogen
> >> bond? In that case you will probably need to write your own script for
> >> it for the time being. I'll try to illustrate why with an example. Say
> >> I want to ask how often is BMR_49.O22 involved in any hydrogen bond as
> >> an acceptor. I could naively sum up the total number of frames the
> >> bond is present (TotFrames) for each instance of this acceptor atom
> >> and then divide by the total number of lifetimes:
> >>
> >> 4 20 5 1.8500 37
> >> BMR_49.O22-BMR_1.O26-H26
> >> 7 28 2 1.0357 29
> >> BMR_49.O22-BMR_1.O13-H13
> >>
> >> the total number frames there is a hydrogen bond is 66, and the total
> >> number of lifetimes is 48, so the average lifetime for BMR_49.O22
> >> involved in any hydrogen bond (given the data here) is 1.375 frames.
> >> However, this is only true if the data were sequential, because it
> >> doesn't take into account the times when one is present and the other
> >> isn't. For example, given this hydrogen bond data (where HB1
> >> represents a single acceptor):
> >>
> >> HB1-1 HB1-2
> >> 1 0
> >> 0 1
> >> 1 0
> >> 1 1
> >>
> >> Using the method I illustrated before you'd come up with an average of
> >> (5 / 4 = 1.25). However, the actual answer of how often is HB1
> >> involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
> >> is broken, HB1-2 is formed, so its always involved in some kind of
> >> hydrogen bond. So to do what you want you will need to write out the
> >> raw time series data, sum up the columns corresponding to the hydrogen
> >> bonds you are interested in, then run 'lifetime' analysis on that data
> >> set. So using the above sets as an example, the set I would actually
> >> run lifetime analysis on would look like:
> >>
> >> (HB1-1)+(HB1-2)
> >> 1
> >> 1
> >> 1
> >> 2
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> On Wed, Mar 11, 2015 at 12:57 AM, Vijay Achari <glycoamber.gmail.com>
> >> wrote:
> >> > Dear Dan,
> >> >
> >> > In my case the time gap in between two frames (taken for analysis) is
> >> 5ps.
> >> >
> >> > #Set Nlifetimes MaxLT AvgLT TotFrames SetName
> >> > 0 17 215 55.7059 947
> >> > BMR_42.O22-BMR_1.O23-H23
> >> > 1 1 1 1.0000 1
> >> > BMR_42.O23-BMR_1.O23-H23
> >> > 2 31 3 1.0968 34
> >> > BMR_31.O22-BMR_1.O26-H26
> >> > 3 11 2 1.0909 12
> >> > BMR_31.O13-BMR_1.O26-H26
> >> > 4 20 5 1.8500 37
> >> > BMR_49.O22-BMR_1.O26-H26
> >> > 5 24 4 1.7917 43
> >> > BMR_49.O23-BMR_1.O26-H26
> >> > 6 41 2 1.0488 43
> >> > BMR_49.O12-BMR_1.O12-H12
> >> > 7 28 2 1.0357 29
> >> > BMR_49.O22-BMR_1.O13-H13
> >> > 8 1 1000 1000.0000 1000
> >> > BMR_49.O13-BMR_1.O13-H13
> >> > 9 1 1 1.0000 1
> >> > BMR_22.O12-BMR_2.O22-H22
> >> > 10 50 62 18.9400 947
> >> > BMR_59.O13-BMR_2.O22-H22
> >> > 11 1 1 1.0000 1
> >> > BMR_59.O25-BMR_2.O23-H23
> >> > 12 34 5 1.1471 39
> >> > BMR_59.O13-BMR_2.O23-H23
> >> > 13 7 6 2.1429 15
> >> > BMR_59.O26-BMR_2.O24-H24
> >> > 14 6 8 3.6667 22
> >> > BMR_59.O25-BMR_2.O24-H24
> >> > 15 28 2 1.1071 31
> >> > BMR_10.O26-BMR_2.O26-H26
> >> > 16 52 121 15.1346 787
> >> > BMR_10.O25-BMR_2.O26-H26
> >> > 17 65 9 1.9231 125
> >> > BMR_10.O13-BMR_2.O26-H26
> >> > 18 4 4 2.2500 9
> >> > BMR_59.O26-BMR_2.O26-H26
> >> > 19 9 1 1.0000 9
> >> > BMR_22.O15-BMR_2.O13-H13
> >> > 20 1 1 1.0000 1
> >> > BMR_10.O11-BMR_2.O16-H16
> >> > 21 7 2 1.1429 8
> >> > BMR_53.O13-BMR_2.O16-H16
> >> > 22 2 3 2.5000 5
> >> > BMR_33.O13-BMR_3.O22-H22
> >> > 23 97 54 6.8247 662
> >> > BMR_61.O26-BMR_3.O22-H22
> >> > 24 1 1 1.0000 1
> >> > BMR_29.O26-BMR_3.O23-H23
> >> > 25 31 36 3.3226 103
> >> > BMR_29.O16-BMR_3.O23-H23
> >> > 26 22 2 1.2273 27
> >> > BMR_30.O22-BMR_3.O23-H23
> >> > 27 4 1 1.0000 4
> >> > BMR_33.O22-BMR_3.O23-H23
> >> > 28 38 2 1.1316 43
> >> > BMR_33.O13-BMR_3.O23-H23
> >> > (there are more than 2000 lines, but I work on only 28 lines to get
> some
> >> > understanding)
> >> >
> >> >
> >> > For clarity, I shall show you how I worked on the given results above.
> >> >
> >> > I want to know the lifetime of HB for O22 (ACCEPTOR) atom only. So, I
> >> did
> >> > in this way,
> >> >
> >> > 1) sum the values from column AvgLT for the only occurrences of O22.
> >> > 2) than find the average of that, where the denominator would be the
> >> number
> >> > of occurrences of O22.
> >> >
> >> > Based on the above steps, the results are :
> >> >
> >> > O22 occur 6 times,
> >> > sum of O22 is 61.916, and
> >> > average of O22 is 10.319.
> >> >
> >> > So, I figured out the lifetime of O22 would be 10.319 x 5ps = 51.595
> >> ps.
> >> >
> >> > Is this correct? Did I choose the correct column "AvgLT"?
> >> >
> >> > I hope to get some feedback if this is correct way to do it.
> >> >
> >> > Many thanks in advance.
> >> >
> >> > Vijay
> >> >
> >> >
> >> > On Wed, Mar 11, 2015 at 11:50 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >
> >> >> On Tue, Mar 10, 2015 at 9:24 PM, Vijay Achari <glycoamber.gmail.com>
> >> >> wrote:
> >> >> > Could you explain on how to get the lifetime value in pico second
> >> (ps)?
> >> >>
> >> >> This depends on how often you recorded your coordinate trajectory.
> For
> >> >> example, say you ran a simulation with a timestep of 2 fs (dt=0.002
> >> >> ps) and you recorded a trajectory frame every 500 steps (ntwx=500).
> >> >> This means that each frame in your trajectory has been recorded at 1
> >> >> ps intervals. However, say you recorded your trajectory every 5000
> >> >> steps instead - your trajectory then will have been recorded at 10 ps
> >> >> intervals. Since lifetimes are always given in frames, it should be
> >> >> easy to convert to ps based on how often your coordinate trajectory
> >> >> was written to (e.g. in the latter case a max lifetime of 1 frame
> >> >> would mean 10 ps).
> >> >>
> >> >> Hope this helps,
> >> >>
> >> >> -Dan
> >> >>
> >> >> >
> >> >> > Thanks in advance.
> >> >> > Vijay
> >> >> >
> >> >> >
> >> >> > On Tue, Mar 10, 2015 at 10:15 PM, Daniel Roe <
> daniel.r.roe.gmail.com
> >> >
> >> >> wrote:
> >> >> >
> >> >> >> Hi,
> >> >> >>
> >> >> >> On Tue, Mar 10, 2015 at 2:53 AM, Vijay Achari <
> glycoamber.gmail.com
> >> >
> >> >> >> wrote:
> >> >> >> > generate two files with lifetime information. The
> >> >> *solute.lifetime.dat*
> >> >> >> contain
> >> >> >> > info like:
> >> >> >> >
> >> >> >> > #Set Nlifetimes MaxLT AvgLT TotFrames
> SetName
> >> >> >> > 0 22 1 1.0000
> 22
> >> >> >> BMR_3.O16-BMR_1.O22-H22
> >> >> >> > 1 296 346 15.6959 4646
> >> >> >> BMR_42.O22-BMR_1.O22-H22
> >> >> >> > 2 992 12 1.4688 1457
> >> >> >> BMR_42.O14-BMR_1.O22-H22
> >> >> >> > 3 1 1 1.0000
> 1
> >> >> >> BMR_42.O13-BMR_1.O22-H22
> >> >> >> > 4 189 12 1.1429 216
> >> >> >> BMR_57.O25-BMR_1.O22-H22
> >> >> >> > 5 462 410 12.3074 5686
> >> >> >> BMR_57.O16-BMR_1.O22-H22
> >> >> >> >
> >> >> >> > I would like to know how I can go from here to calculate the
> >> >> hb-lifetime
> >> >> >> between
> >> >> >> > solute and solute?
> >> >> >>
> >> >> >> I'm not really sure I understand your question. The data output
> you
> >> >> >> posted is exactly the lifetime calculation. For example, the
> second
> >> >> >> set (1) contains lifetime information for the hydrogen bond
> between
> >> >> >> residue 42, atom O22 and residue 1, atoms O22-H22; there were 296
> >> >> >> individual lifetimes (i.e. the hbond formed 296 times), the max of
> >> >> >> which lasted 346 frames, the average lifetime is ~15.7 frames. Let
> >> me
> >> >> >> know if I'm not understanding you or if I can explain more.
> >> >> >>
> >> >> >> -Dan
> >> >> >>
> >> >> >> >
> >> >> >> > I have read the pages 556-557 from AMBER 14 manual, but I find
> it
> >> >> >> difficult
> >> >> >> > to see how one should start processing and getting the lifetime
> >> value.
> >> >> >> >
> >> >> >> > I think simple example would help me much in this case.
> >> >> >> >
> >> >> >> > Could you give me some example on how this can be obtained?
> >> >> >> >
> >> >> >> > Your help is much appreciated.
> >> >> >> >
> >> >> >> > Thank you.
> >> >> >> > Vijay
> >> >> >> > _______________________________________________
> >> >> >> > AMBER mailing list
> >> >> >> > AMBER.ambermd.org
> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> -------------------------
> >> >> >> Daniel R. Roe, PhD
> >> >> >> Department of Medicinal Chemistry
> >> >> >> University of Utah
> >> >> >> 30 South 2000 East, Room 307
> >> >> >> Salt Lake City, UT 84112-5820
> >> >> >> http://home.chpc.utah.edu/~cheatham/
> >> >> >> (801) 587-9652
> >> >> >> (801) 585-6208 (Fax)
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> -------------------------
> >> >> Daniel R. Roe, PhD
> >> >> Department of Medicinal Chemistry
> >> >> University of Utah
> >> >> 30 South 2000 East, Room 307
> >> >> Salt Lake City, UT 84112-5820
> >> >> http://home.chpc.utah.edu/~cheatham/
> >> >> (801) 587-9652
> >> >> (801) 585-6208 (Fax)
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> ------------------------------
>
> Message: 25
> Date: Mon, 16 Mar 2015 14:26:16 -0300
> From: George Tzotzos <gtzotzos.me.com>
> Subject: [AMBER] ante-mmpbsa.py: problem with the mask syntax
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <9AC7A9A5-FE58-4AB2-BDFE-7E1EFC841671.me.com>
> Content-Type: text/plain; charset=windows-1252
>
> I?m working on a homodimer that includes two identical ligands (one per
> subunit) as well as two conserved water molecules.
>
> Each subunit consists of 125 residues (subA residues 1-125, subB residues:
> 127-151), the ligands residues are 126 and 152 and the conserved waters
> residues 253 and 254.
>
> CASE 1.
>
> I?m using the following ante-mmpbsa script to generate topology files:
>
> ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop
> -l subB.prmtop -s :WAT,Na+,&!:253-254 -n :127-252,254 --radii=mbondi2
>
> Apparently the syntax of the strip mask -s :WAT,Na+,&!:253-254 is wrong
> and the error message given is -bash: :253-254: bad word specifier
>
> CASE 2.
>
> Script
>
> ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop
> -l subB.prmtop -s :WAT,Na+,:126,:152 -n :127-251 --radii=mbondi2
>
> Also same as above but modifying the mask of the above to: -s
> :WAT,Na+,:126,152
>
> produced topologies the same topologies: (a) subA-subB containing 250
> residues, 4 molecules; (b) subA containing 126 residues, 2 molecules; (c)
> subB containing 124 residues, 3 molecules
>
> Any suggestions on correcting this would be most helpful
>
> Regards
>
> George
>
>
>
>
>
>
> ------------------------------
>
> Message: 26
> Date: Tue, 17 Mar 2015 01:49:31 +0800
> From: Vijay Achari <glycoamber.gmail.com>
> Subject: Re: [AMBER] finding angles
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CA+-itZg8z217qqYQjoaaZnzN7sharheW5k+aVXjdrVAG8XS0Ag.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> HI Dan,
>
> The command I used was:
>
>
>
> for i in {1..128};do
>
> cpptraj $top <<EOF
> trajin $path/reImaged-bcmLyo25perR.nc 15001 60000 #60000
>
> vector v1 principal z
> vector v2 :$i.C52 :$i.C61
> vector v3 :$i.C64 :$i.C69
>
> vectormath vec1 v1 vec2 v2 out dataFiles-only/angleZ-chainC12-lipid-$i.dat
> name AngleZ-C12 dotangle
> vectormath vec1 v1 vec2 v3 out dataFiles-only/angleZ-chainC8-lipid-$i.dat
> name AngleZ-C8 dotangle
>
> EOF
>
> done
>
>
>
> Previously there was white space after z. That's why it showed [z ] in the
> error before. Once the white space fixed, the calculation run fine.
>
> Thanks for your kind help and guide.
>
> Best reagards
> Vijay
>
> On Mon, Mar 16, 2015 at 9:58 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > That shouldn't happen since cpptraj removes whitespace from input
> commands.
> > Are you enclosing your input commands in quotes or something?
> >
> > -Dan
> >
> > On Monday, March 16, 2015, Vijay Achari <glycoamber.gmail.com> wrote:
> >
> > > There was a space after "z", as below:
> > > [vector v1 principal z ]
> > >
> > > This should be
> > >
> > > [vector v1 principal z]
> > >
> > > Regards
> > >
> > >
> > >
> > >
> > >
> > > On Fri, Mar 13, 2015 at 11:40 AM, Vijay Achari <glycoamber.gmail.com
> > > <javascript:;>> wrote:
> > >
> > > > OK,
> > > >
> > > > Let me update the cpptraj and test it again.
> > > > Vj
> > > >
> > > > On Fri, Mar 13, 2015 at 11:15 AM, Daniel Roe <daniel.r.roe.gmail.com
> > > <javascript:;>>
> > > > wrote:
> > > >
> > > >> On Thu, Mar 12, 2015 at 7:24 PM, Vijay Achari <glycoamber.gmail.com
> > > <javascript:;>>
> > > >> wrote:
> > > >> > [vector v1 principal z ]
> > > >> > VECTOR: Type Principal X, mask [*]
> > > >> > Error: [vector] Not all arguments handled: [ z ]
> > > >>
> > > >> That's weird - when I run the same command I get:
> > > >>
> > > >> > vector v1 principal z
> > > >> VECTOR: Type Principal Z, mask [*]
> > > >>
> > > >> I notice that your CPPTRAJ is a bit out of date. Try updating to the
> > > >> latest version (14.25) and see if that helps. Also make sure all of
> > > >> your cpptraj test cases are passing.
> > > >>
> > > >> -Dan
> > > >>
> > > >> > 1 errors encountered reading input.
> > > >> > TIME: Total execution time: 0.0568 seconds.
> > > >> >
> > > >> > vijay.micelle
> > > >>
> > >
> >
> :~/Simulation/chapter6-lyo-paper3-Vj/lyo-Analysis2/struc-10-tail-to-Z-angle-distribution/Chain-Angle-distribution-betaLyo25perR$
> > > >> >
> > > >> >
> > > >> > Thank you.
> > > >> >
> > > >> > On Thu, Mar 12, 2015 at 11:20 PM, Daniel Roe <
> > daniel.r.roe.gmail.com
> > > <javascript:;>>
> > > >> wrote:
> > > >> >
> > > >> >> Hi,
> > > >> >>
> > > >> >> On Thu, Mar 12, 2015 at 8:00 AM, Vijay Achari <
> > glycoamber.gmail.com
> > > <javascript:;>>
> > > >> >> wrote:
> > > >> >> > *vector v1 principal z vector v2 :1.C50 :1.C80vectormath
> vec1
> > > v1
> > > >> >> vec2
> > > >> >> > v2 out vectorTimesdat name chainAngle dotangle*
> > > >> >> > But I get error.
> > > >> >>
> > > >> >> Your input is mangled - seems like your newlines are not making
> it
> > to
> > > >> >> your email. Make sure you're sending everything in plain text
> mode.
> > > >> >> Also, don't just say you got an "error" - actually report the
> > *exact*
> > > >> >> error message, otherwise our chances of effectively helping you
> are
> > > >> >> slim.
> > > >> >>
> > > >> >> -Dan
> > > >> >>
> > > >> >> --
> > > >> >> -------------------------
> > > >> >> Daniel R. Roe, PhD
> > > >> >> Department of Medicinal Chemistry
> > > >> >> University of Utah
> > > >> >> 30 South 2000 East, Room 307
> > > >> >> Salt Lake City, UT 84112-5820
> > > >> >> http://home.chpc.utah.edu/~cheatham/
> > > >> >> (801) 587-9652
> > > >> >> (801) 585-6208 (Fax)
> > > >> >>
> > > >> >> _______________________________________________
> > > >> >> AMBER mailing list
> > > >> >> AMBER.ambermd.org <javascript:;>
> > > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >> >>
> > > >> > _______________________________________________
> > > >> > AMBER mailing list
> > > >> > AMBER.ambermd.org <javascript:;>
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> -------------------------
> > > >> Daniel R. Roe, PhD
> > > >> Department of Medicinal Chemistry
> > > >> University of Utah
> > > >> 30 South 2000 East, Room 307
> > > >> Salt Lake City, UT 84112-5820
> > > >> http://home.chpc.utah.edu/~cheatham/
> > > >> (801) 587-9652
> > > >> (801) 585-6208 (Fax)
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org <javascript:;>
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 27
> Date: Mon, 16 Mar 2015 13:53:12 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] finding angles
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qrQQLbjFTz7gTaDg8Ts57=
> 6Tnk6VWSTKL1cUvk8ZkUfQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Mar 16, 2015 at 1:49 PM, Vijay Achari <glycoamber.gmail.com>
> wrote:
>
> > HI Dan,
> >
> > The command I used was:
> >
> >
> >
> > for i in {1..128};do
> >
> > cpptraj $top <<EOF
> > trajin $path/reImaged-bcmLyo25perR.nc 15001 60000 #60000
> >
> > vector v1 principal z
> > vector v2 :$i.C52 :$i.C61
> > vector v3 :$i.C64 :$i.C69
> >
> > vectormath vec1 v1 vec2 v2 out
> dataFiles-only/angleZ-chainC12-lipid-$i.dat
> > name AngleZ-C12 dotangle
> > vectormath vec1 v1 vec2 v3 out
> dataFiles-only/angleZ-chainC8-lipid-$i.dat
> > name AngleZ-C8 dotangle
> >
> > EOF
> >
> > done
> >
> >
> >
> > Previously there was white space after z. That's why it showed [z ] in
> the
> > error before. Once the white space fixed, the calculation run fine.
> >
>
> ?What kind of whitespace was it? Was it a carriage return? A tab?
> cpptraj splits argument lists on whitespace. So it's possible that *some*
> whitespace characters (like weird half-DOS-line-endings, tabs, or something
> else?) that *renders* as whitespace could cause this problem.
>
> It would be nice to know what that character was, though, so this problem
> can be fixed.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 28
> Date: Mon, 16 Mar 2015 14:21:13 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com>
> Subject: Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CALeh7kB83dLfrD1LmvnPHiohC3e=
> poY4K4hAUrewtKSnFPybhw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> George,
>
> Each subunit consists of 125 residues (subA residues 1-125, subB residues:
> > 127-151), the ligands residues are 126 and 152 and the conserved waters
> > residues 253 and 254.
> >
>
> I'm confused by the numbering of your atoms- shouldn't subB be 127-251, and
> the second ligand at 252? You may want to double check, since that's what
> could be throwing it off.
>
> But you can try-
>
> ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop -l
> subB.prmtop -s :WAT,:Na+ -n :1-126,:253 --radii=mbondi2
>
> Which should give you the subunits with the ligands and water molecules,
> assuming that 253 is the corresponding water for the first subunit. I can't
> speak for the syntax error, though.
>
>
> For the second case, which looks like you want both dimers without their
> respective water molecules and ligands? If so, you can try-
>
> ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop -l
> subB.prmtop -s :WAT,:Na+,:126,:252,:253-254 -n :1-125 --radii=mbondi2
>
> Best,
>
> Kenneth
>
> On Mon, Mar 16, 2015 at 1:26 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
> > I?m working on a homodimer that includes two identical ligands (one per
> > subunit) as well as two conserved water molecules.
> >
> > Each subunit consists of 125 residues (subA residues 1-125, subB
> residues:
> > 127-151), the ligands residues are 126 and 152 and the conserved waters
> > residues 253 and 254.
> >
> > CASE 1.
> >
> > I?m using the following ante-mmpbsa script to generate topology files:
> >
> > ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop
> > -l subB.prmtop -s :WAT,Na+,&!:253-254 -n :127-252,254 --radii=mbondi2
> >
> > Apparently the syntax of the strip mask -s :WAT,Na+,&!:253-254 is wrong
> > and the error message given is -bash: :253-254: bad word specifier
> >
> > CASE 2.
> >
> > Script
> >
> > ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r subA.prmtop
> > -l subB.prmtop -s :WAT,Na+,:126,:152 -n :127-251 --radii=mbondi2
> >
> > Also same as above but modifying the mask of the above to: -s
> > :WAT,Na+,:126,152
> >
> > produced topologies the same topologies: (a) subA-subB containing 250
> > residues, 4 molecules; (b) subA containing 126 residues, 2 molecules; (c)
> > subB containing 124 residues, 3 molecules
> >
> > Any suggestions on correcting this would be most helpful
> >
> > Regards
> >
> > George
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
>
>
> ------------------------------
>
> Message: 29
> Date: Mon, 16 Mar 2015 14:37:47 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
> To: amber.ambermd.org
> Message-ID: <1426531067.12101.26.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2015-03-16 at 14:26 -0300, George Tzotzos wrote:
> > I?m working on a homodimer that includes two identical ligands (one
> > per subunit) as well as two conserved water molecules.
> >
> > Each subunit consists of 125 residues (subA residues 1-125, subB
> > residues: 127-151), the ligands residues are 126 and 152 and the
> > conserved waters residues 253 and 254.
> >
> > CASE 1.
> >
> > I?m using the following ante-mmpbsa script to generate topology files:
> >
> > ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r
> > subA.prmtop -l subB.prmtop -s :WAT,Na+,&!:253-254 -n :127-252,254
> > --radii=mbondi2
> >
> > Apparently the syntax of the strip mask -s :WAT,Na+,&!:253-254 is
> > wrong and the error message given is -bash: :253-254: bad word
> > specifier
>
> Actually, this is the shell assigning special meaning to the bang (!)
> character. If you want to use it as a character in a command-line, you
> need to enclose that particular argument in quotations so the shell
> knows not to invoke its special meaning:
>
> ante-MMPBSA.py -p complex_solv.prmtop -c subA-subB.prmtop \
> -r subA.prmtop -l subB.prmtop -s ':WAT,Na+&!:253-254' \
> -n :127-252,254 --radii=mbondi2
> >
> > CASE 2.
> >
> > Script
> >
> > ante-mmpbsa.py -p complex_solv.prmtop -c subA-subB.prmtop -r
> > subA.prmtop -l subB.prmtop -s :WAT,Na+,:126,:152 -n :127-251
> > --radii=mbondi2
> >
> > Also same as above but modifying the mask of the above to: -s :WAT,Na
> > +,:126,152
> >
> > produced topologies the same topologies: (a) subA-subB containing 250
> > residues, 4 molecules; (b) subA containing 126 residues, 2 molecules;
> > (c) subB containing 124 residues, 3 molecules
> >
> > Any suggestions on correcting this would be most helpful
>
> This has to do with atoms and residues getting 'renumbered' following
> the strip_mask. When you delete residue number 126, the residue that
> *was* 127 in the solvated complex is 126 in the stripped complex (from
> which the ligand and receptor files are generated). Kenneth's
> suggestion is the best approach to dodge this renumbering issue
> completely.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1160, Issue 1
> **************************************
>
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Received on Tue Mar 17 2015 - 02:00:02 PDT