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------------------------------
Message: 5
Date: Thu, 9 Apr 2015 00:59:13 -0400
From: Kenneth Huang <kennethneltharion.gmail.com>
Subject: Re: [AMBER] MMBP(GB)SA free energy decomposition error:
sander failed with prmtop
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CALeh7kDYuMbgXVgVhNxVMsOOOEUL7C-zUCDt-EMiGS93v3YUdg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Maryam,
Try checking the MMPBSA_complex_pb.mdout file- it'll have a more
descriptive error message than what you're seeing right now, and help
pinpoint exactly what's going wrong.
Best,
Kenneth
On Wed, Apr 8, 2015 at 11:40 PM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> Dear All,
> I am trying to run per-residue free energy decomposition for a ligand (46
> a.a) using Amber12. But I got this error which argues with my non solvated
> complex topology file:
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> sander found! Using /usr/local/packages/amber12/amber12/bin/sander
> mmpbsa_py_energy found! Using
> /usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
>
> Beginning PB calculations with
> /usr/local/packages/amber12/amber12/bin/sander
> calculating complex contribution...
> *CalcError: /usr/local/packages/amber12/amber12/bin/sander failed with
> prmtop structure_no_wat.parm7!*
>
> will you guide me how to fix this problem?
> I attached the input and the parm file.
> Best Regards,
> Maryam
>
> _______________________________________________
> 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: 6
Date: Thu, 9 Apr 2015 01:22:52 -0400
From: Laura Tociu <ltociu.princeton.edu>
Subject: Re: [AMBER] MMPBSA.py.MPI Installation Failure
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CANThz_jtEeHv02z-d501gbGuEg6VrjPxsCFfCTdN1vgphJ31PA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Thanks Jason!
Installing Amber in serial does the trick. Apparently MMPBSA.py did install
correctly despite that error.
Best,
Laura
---------- Forwarded message ----------
From: Jason Swails <jason.swails.gmail.com>
Date: Tue, Apr 7, 2015 at 11:36 AM
Subject: Re: [AMBER] MMPBSA.py.MPI Installation Failure
To: AMBER Mailing List <amber.ambermd.org>
On Sat, Apr 4, 2015 at 2:34 PM, Laura Tociu <ltociu.princeton.edu> wrote:
> Hi,
>
> I recently installed Amber14 and AmberTools14. I followed instructions
from
> the IT guys from my group, and did:
>
> tar jxvf AmberTools14.tar.bz2
> tar jxvf Amber14.tar.bz2
> cd amber14
> export AMBERHOME=`pwd`
>
> module purge
>
> module load openmpi
>
> export MKL_HOME=/opt/intel/composer_xe_2013_sp1.0.080/mkl
>
> ./configure -mpi intel
> make install
>
> echo "source $AMBERHOME/amber.sh" >> ~/.bashrc
>
>
> I used MKL because I wanted to decrease the computational time required by
> QM/MM molecular dynamics. I've been able to run QM/MM MD succesfully, but
> as I am now getting ready to start binding energy calculations, I realized
> that MMPBSA did not install correctly. There is no mmpbsa_py_energy in
> $AMBERHOME/bin so I am getting the error that mmpbsa_py_energy could not
be
> found.
>
> I am attaching the mpi4py_install.log file. There seems to be an error in
> there related to mpe.h. I don't really know what other information might
be
> helpful. Let me know what other files might be useful and I will attach
> them.
>
?Google searches suggest to me that MPE is an optional component of OpenMPI
(or maybe the MPI standard itself, I'm not sure). But it doesn't seem to
be installed. Suggested solutions are to either "install MPE" or "build
without it". I'm not sure how to do either of these.
Here are some suggestions:
Build in serial as well? -- mmpbsa_py_energy is only built in serial.
MMPBSA.py.MPI itself is parallel, but each thread calls a serial program to
evaluate energies.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 7
Date: Thu, 09 Apr 2015 09:00:32 +0200
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] FW: TLEAP Fatal Error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20150409090032.e41ff88gkcwo0o8k.webmail.u-picardie.fr>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Dear Sook Wong,
> I am trying to generate the parameters for attached PDB without
> success as my command line is showing below:
>
> FATAL: Atom .R<POT 4875>.A<POT 1> does not have a type.
> FATAL: Atom .R<POT 4876>.A<POT 1> does not have a type.
> FATAL: Atom .R<CLA 4877>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4878>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4879>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4880>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4881>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4882>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4883>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4884>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4885>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4886>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4887>.A<CLA 1> does not have a type.
> FATAL: Atom .R<CLA 4888>.A<CLA 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> Can anyone explain how to resolve this problem? Appreciated.
If you use PyRED at R.E.D. Server Dev.
http://q4md-forcefieldtools.org/REDServer-Development/ an entire force
field (FF) is generated for the input molecules and a LEaP script is
created allowing the user to directly use the generated FF.
see a simple case at: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#6
tar -jxvf P$x.tar.bz2
cd P$x/Data-R.E.D.Server/Data-Default-Proj
xleap -f leaprc.q4mdfft
all the commands available in this LEaP script has an Amber reference
to the html documentation; i.e. http://ambermd.org/doc6/leap.html
thus any user has a direct access to the web page for each LEaP command...
an atom type has to be declared before to be loaded...
regards, Francois
------------------------------
Message: 8
Date: Thu, 9 Apr 2015 10:22:29 +0100
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Subject: Re: [AMBER] error generating P450 prmtop incrd file
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAO6-0Tmkzo1Yn8G-hk6SoDE2AiAo-t8PbjVd-jiLDEuuaCAqDg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi All,
Based on the suggestion by Jason, the following bond command has worked and
I am able to see the bond between Fe and S after loading the prmtop and
inpcrd file in vmd.
It looks like the files are ready for simulation. :)
bond P450.419.SG P450.477.FE
Thank you all.
Cheers.
Vaibhav
On Wed, Apr 8, 2015 at 6:08 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Apr 8, 2015 at 1:06 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> >
> >
> > On Wed, Apr 8, 2015 at 11:33 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> > wrote:
> >
> >> Hi All,
> >> I have followed the procedure suggested and used the following modified
> >> leap input file and it seems to work except for the fact that bond
> between
> >> S and Fe is not formed.
> >> Can you please suggest on the correct usage for "bond" command? I have
> >> tried "bond P450.6768.SG P450.7755.FE 1", "bond 6768 7755 1" but got
> the
> >>
> >
> > ?The second number should be the *residue* number, not the atom number.
> >
>
> ?Sorry, I'll clarify:
>
> P450.6768.SG
>
> The above means look at the 6768th residue of the P450 unit (which you
> defined via loadPDB), and take the atom named SG from the residue you
> selected (the 6768th residue).
>
> The second proposed syntax: "bond 6768 7755 1" is wrong. tleap doesn't
> know that "6768" or "7755" are atom numbers... or what system they would
> correspond to, anyway.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
??Please consider the environment before printing this e-mail
------------------------------
Message: 9
Date: Thu, 9 Apr 2015 13:14:54 +0300
From: Michael Shokhen <michael.shokhen.biu.ac.il>
Subject: Re: [AMBER] Error in tutorial A16, Amber 14
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAMyFEY5cbMA32egj-QfsQcn2Xt6tse1gMwi8ngtzZMeaVGqZdw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi Ben,
Thank you for your comment:
The error message indicates that one of your residues in your PDB has an
incorrect number of atoms. This is one of
the checks that the script does on the molecules while processing it.
Basically, the script does a substitution on each
atom in the residue and if it finds the incorrect number of atoms then it
stops.
It well correlates with the error message from charmmlipid2amber.py:
Error: Number of atoms in residue does not match number of atoms in residue
in replacement data file
Unfortunately your comment and the error message are too general to work
the problem around.
I can't find any specific place of incorrect atom number in the
step5_assembly.pdb file that causes the error, because the atom numbers are
smoothly increasing from 1 to 91154 as generated by Charmm-Gui.
Regarding the recommended in the A16 tutorial TER insertion after protein.
In original step5_assembly.pdb generated by Charmm-Gui there is no TER
after protein:
ATOM 5461 OT1 ALA 348 -10.030 -0.328 -36.334 1.00 0.00 PROA
ATOM 5462 OT2 ALA 348 -9.337 -1.565 -38.055 1.00 0.00 PROA
ATOM 5463 C3 CHL1 1 -28.933 18.011 17.293 1.00 0.00 MEMB
ATOM 5464 H3 CHL1 1 -27.890 18.323 17.067 1.00 0.00 MEMB
Following the A16 tutorial direction I have added it manually by text
editor:
ATOM 5461 OT1 ALA 348 -10.030 -0.328 -36.334 1.00 0.00 PROA
ATOM 5462 OT2 ALA 348 -9.337 -1.565 -38.055 1.00 0.00 PROA
TER
ATOM 5463 C3 CHL1 1 -28.933 18.011 17.293 1.00 0.00 MEMB
ATOM 5464 H3 CHL1 1 -27.890 18.323 17.067 1.00 0.00 MEMB
You see that indeed there is an interruption in atom numbers in the TER row
which doesn't contain any atom number in contrast to the standard PDB
format where
it shoud be: TER 5463 ALA 348
Unfortunately, I can't manually renumber all remaining ~90000 atoms after
TER by text editor,
so I used Chimera software to correct the situation:
ATOM 5461 OT1 ALA 348 -10.030 -0.328 -36.334 1.00 0.00 O
ATOM 5462 OT2 ALA 348 -9.337 -1.565 -38.055 1.00 0.00 O
TER 5463 ALA 348
HETATM 5464 C3 CHL1 1 -28.933 18.011 17.293 1.00 0.00 C
HETATM 5465 H3 CHL1 1 -27.890 18.323 17.067 1.00 0.00 H
As you can see the Chimera changes the original format of Charmm-Gui,
that could be a potential error origin.
I have examined all three variants of PDB file. The answer from
charmmlipid2amber.py was absolutely identical:
Error:
Number of atoms in residue does not match number of atoms in residue
in replacement data file
I would appreciate any your help in the problem solution.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
On Thu, Apr 9, 2015 at 6:15 AM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> Hi Michael,
>
> The error message indicates that one of your residues in your PDB has an
> incorrect number of atoms. This is one of the checks that the script does
> on the molecules while processing it. Basically, the script does a
> substitution on each atom in the residue and if it finds the incorrect
> number of atoms then it stops.
>
> Residues are split in the PDB by the residue number field of the PDB and
> identified by the residue sequence field and TER cards. The script only
> processes C36 lipids, water, and some ions. All other residues are ignored.
>
> So, first check if the residues to be converted (lipids, water, ions)
> match the template of substitution file (charmmlipid2amber.csv). If there
> is no problem there, then it is probably a problem with residue sequence or
> TER. The script assumes that the normal PDB residue sequence and TER cards
> are used.
>
> Best,
> Ben
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 10
Date: Thu, 9 Apr 2015 12:15:09 +0100
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Subject: [AMBER] larger bonds between protein atoms
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAO6-0TnvER30Bd5TdfXU9AGVvgHCMJ+FkbrkP8H7QnH636VA9w.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi All,
I have prepared prmtop and inpcrd files as discussed in a recent thread
(can't find the link in the archive yet).
But I am getting strange warnings from tleap that there are large bonds
between atoms of the same residues (protein and ligand).
I have checked the coordinates for a couple of them and this doesn't look
to be the case.
Can you please take a look and suggest me if these are due to bad pdb
structure or some other error?
Thanks a lot.
ukmcdwlx005 189% tleap -s -f leap.in
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/prep to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/lib to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/parm to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap.in.
Welcome to LEaP!
Sourcing: ./leap.in
----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB
----- Source of
/apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_nucleic94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_amino94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminoct94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminont94.lib
Loading library: /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/ions94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/solvents.lib
----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
----- Source of /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010)
add. info. at the end
Loading Mol2 file: ./CYS_HS.mol2
Reading MOLECULE named CYP-IC6
UNIT name: CYP-IC6
Head atom: .R<CYP 1>.A<N 1>
Tail atom: .R<CYP 1>.A<C 9>
Contents:
R<CYP 1>
Loading Mol2 file: ./HEM_pentacoordinateHS.mol2
Reading MOLECULE named HEM-IC6
Loading parameters: ./HEM_HS.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Mol2 file: ./ERY.mol2
Reading MOLECULE named ERY
Loading parameters: ./ERY.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading PDB file: ./2J0D_prepared1.pdb
(starting new molecule for chain 1)
(starting new molecule for chain 2)
(starting new molecule for chain 3)
(starting new molecule for chain 4)
Added missing heavy atom: .R<CTYR 99>.A<OXT 22>
Added missing heavy atom: .R<CPRO 199>.A<OXT 15>
Added missing heavy atom: .R<CSER 299>.A<OXT 12>
Added missing heavy atom: .R<CTYR 399>.A<OXT 22>
Added missing heavy atom: .R<CARG 496>.A<OXT 25>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NB-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NA-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-ND-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NC-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 3868
Leap added 3970 missing atoms according to residue templates:
5 Heavy
3965 H / lone pairs
Scaling up box by a factor of 1.252551 to meet diagonal cut criterion
Solute vdw bounding box: 77.194 75.259 55.253
Total bounding box for atom centers: 107.256 107.256 107.256
(box expansion for 'iso' is 28.0%)
Solvent unit box: 18.774 18.774 18.774
Volume: 634337.815 A^3 (oct)
Total mass 340597.068 amu, Density 0.892 g/cc
Added 15848 residues.
Total unperturbed charge: 3.005998
Total perturbed charge: 3.005998
3 Cl- ions required to neutralize.
Adding 3 counter ions to "P450" using 1A grid
Grid extends from solute vdw + 2.47 to 8.47
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 16 sec
(Replacing solvent molecule)
Placed Cl- in P450 at (-14.72, -8.49, 1.48).
(Replacing solvent molecule)
Placed Cl- in P450 at (12.49, 10.65, -22.81).
(Replacing solvent molecule)
Placed Cl- in P450 at (-22.20, -7.90, 26.79).
Done adding ions.
> saveamberparam P450 P450_2J0D.prmtop P450_2J0D.inpcrd
ERROR: syntax error
> saveamberparm P450 P450_2J0D.prmtop P450_2J0D.inpcrd
Checking Unit.
WARNING: There is a bond of 20.901524 angstroms between:
------- .R<CYS 58>.A<CB 5> and .R<CYS 58>.A<SG 8>
WARNING: There is a bond of 20.837498 angstroms between:
------- .R<MET 59>.A<SD 11> and .R<MET 59>.A<CE 12>
WARNING: There is a bond of 18.891764 angstroms between:
------- .R<CTYR 99>.A<N 1> and .R<CTYR 99>.A<CA 3>
WARNING: There is a bond of 19.115078 angstroms between:
------- .R<NSER 100>.A<C 12> and .R<VAL 101>.A<N 1>
WARNING: There is a bond of 20.475057 angstroms between:
------- .R<NSER 100>.A<CB 7> and .R<NSER 100>.A<OG 10>
WARNING: There is a bond of 19.923242 angstroms between:
------- .R<THR 103>.A<N 1> and .R<THR 103>.A<CA 3>
WARNING: There is a bond of 19.727978 angstroms between:
------- .R<ASN 104>.A<CA 3> and .R<ASN 104>.A<C 13>
WARNING: There is a bond of 20.807121 angstroms between:
------- .R<ARG 105>.A<C 23> and .R<ARG 105>.A<O 24>
WARNING: There is a bond of 20.885143 angstroms between:
------- .R<ARG 106>.A<CA 3> and .R<ARG 106>.A<C 23>
WARNING: There is a bond of 18.744920 angstroms between:
------- .R<PHE 108>.A<CE2 15> and .R<PHE 108>.A<CD2 17>
WARNING: There is a bond of 19.774763 angstroms between:
------- .R<PHE 108>.A<CE1 11> and .R<PHE 108>.A<CZ 13>
WARNING: There is a bond of 19.775034 angstroms between:
------- .R<VAL 111>.A<C 15> and .R<GLY 112>.A<N 1>
WARNING: There is a bond of 19.894110 angstroms between:
------- .R<VAL 111>.A<CA 3> and .R<VAL 111>.A<C 15>
WARNING: There is a bond of 20.054649 angstroms between:
------- .R<GLY 112>.A<C 6> and .R<GLY 112>.A<O 7>
WARNING: There is a bond of 19.604853 angstroms between:
------- .R<GLY 112>.A<N 1> and .R<GLY 112>.A<CA 3>
WARNING: There is a bond of 20.685790 angstroms between:
------- .R<LYS 115>.A<C 21> and .R<SER 116>.A<N 1>
WARNING: There is a bond of 19.905225 angstroms between:
------- .R<LYS 115>.A<N 1> and .R<LYS 115>.A<CA 3>
WARNING: There is a bond of 19.541382 angstroms between:
------- .R<SER 119>.A<C 10> and .R<SER 119>.A<O 11>
WARNING: There is a bond of 21.170183 angstroms between:
------- .R<ILE 120>.A<CB 5> and .R<ILE 120>.A<CG1 11>
WARNING: There is a bond of 19.438126 angstroms between:
------- .R<ILE 120>.A<N 1> and .R<ILE 120>.A<CA 3>
WARNING: There is a bond of 20.260686 angstroms between:
------- .R<ARG 128>.A<CD 11> and .R<ARG 128>.A<NE 14>
WARNING: There is a bond of 19.588907 angstroms between:
------- .R<ARG 128>.A<CG 8> and .R<ARG 128>.A<CD 11>
WARNING: There is a bond of 18.918132 angstroms between:
------- .R<ARG 128>.A<CB 5> and .R<ARG 128>.A<CG 8>
WARNING: There is a bond of 20.067992 angstroms between:
------- .R<ARG 128>.A<CA 3> and .R<ARG 128>.A<C 23>
WARNING: There is a bond of 20.398286 angstroms between:
------- .R<ARG 130>.A<NE 14> and .R<ARG 130>.A<CZ 16>
WARNING: There is a bond of 20.032240 angstroms between:
------- .R<PHE 137>.A<C 19> and .R<THR 138>.A<N 1>
WARNING: There is a bond of 18.979897 angstroms between:
------- .R<PHE 137>.A<CE1 11> and .R<PHE 137>.A<CZ 13>
WARNING: There is a bond of 19.799136 angstroms between:
------- .R<PHE 137>.A<CG 8> and .R<PHE 137>.A<CD1 9>
WARNING: There is a bond of 19.707132 angstroms between:
------- .R<PHE 137>.A<CA 3> and .R<PHE 137>.A<C 19>
WARNING: There is a bond of 20.042140 angstroms between:
------- .R<THR 138>.A<CA 3> and .R<THR 138>.A<CB 5>
WARNING: There is a bond of 20.227088 angstroms between:
------- .R<THR 138>.A<N 1> and .R<THR 138>.A<CA 3>
WARNING: There is a bond of 19.732610 angstroms between:
------- .R<GLY 140>.A<C 6> and .R<LYS 141>.A<N 1>
WARNING: There is a bond of 20.251158 angstroms between:
------- .R<LYS 141>.A<C 21> and .R<LEU 142>.A<N 1>
WARNING: There is a bond of 19.821723 angstroms between:
------- .R<GLU 144>.A<C 14> and .R<MET 145>.A<N 1>
WARNING: There is a bond of 20.209895 angstroms between:
------- .R<GLU 144>.A<N 1> and .R<GLU 144>.A<CA 3>
WARNING: There is a bond of 19.333100 angstroms between:
------- .R<MET 145>.A<CB 5> and .R<MET 145>.A<CG 8>
WARNING: There is a bond of 20.073760 angstroms between:
------- .R<ILE 148>.A<CA 3> and .R<ILE 148>.A<CB 5>
WARNING: There is a bond of 19.781674 angstroms between:
------- .R<TYR 152>.A<CZ 13> and .R<TYR 152>.A<OH 14>
WARNING: There is a bond of 19.835748 angstroms between:
------- .R<ILE 184>.A<CA 3> and .R<ILE 184>.A<C 18>
WARNING: There is a bond of 19.502835 angstroms between:
------- .R<ILE 193>.A<C 18> and .R<ILE 193>.A<O 19>
WARNING: There is a bond of 20.676382 angstroms between:
------- .R<ASP 194>.A<N 1> and .R<ASP 194>.A<CA 3>
WARNING: There is a bond of 20.836815 angstroms between:
------- .R<ASN 198>.A<C 13> and .R<CPRO 199>.A<N 1>
WARNING: There is a bond of 19.207179 angstroms between:
------- .R<NGLN 200>.A<CA 5> and .R<NGLN 200>.A<CB 7>
WARNING: There is a bond of 19.750778 angstroms between:
------- .R<LYS 208>.A<CB 5> and .R<LYS 208>.A<CG 8>
WARNING: There is a bond of 20.549701 angstroms between:
------- .R<LEU 211>.A<CA 3> and .R<LEU 211>.A<CB 5>
WARNING: There is a bond of 20.359004 angstroms between:
------- .R<LEU 211>.A<CA 3> and .R<LEU 211>.A<C 18>
WARNING: There is a bond of 21.048016 angstroms between:
------- .R<ARG 212>.A<CA 3> and .R<ARG 212>.A<C 23>
WARNING: There is a bond of 18.933685 angstroms between:
------- .R<ASP 214>.A<CA 3> and .R<ASP 214>.A<CB 5>
WARNING: There is a bond of 20.530980 angstroms between:
------- .R<PHE 215>.A<C 19> and .R<LEU 216>.A<N 1>
WARNING: There is a bond of 20.628045 angstroms between:
------- .R<PHE 219>.A<C 19> and .R<PHE 220>.A<N 1>
WARNING: There is a bond of 20.406414 angstroms between:
------- .R<PHE 219>.A<CE2 15> and .R<PHE 219>.A<CD2 17>
WARNING: There is a bond of 19.251968 angstroms between:
------- .R<PHE 219>.A<CE1 11> and .R<PHE 219>.A<CZ 13>
WARNING: There is a bond of 20.229592 angstroms between:
------- .R<PHE 219>.A<CA 3> and .R<PHE 219>.A<CB 5>
WARNING: There is a bond of 28.335125 angstroms between:
------- .R<PHE 220>.A<CE2 15> and .R<PHE 220>.A<CD2 17>
WARNING: There is a bond of 27.975862 angstroms between:
------- .R<PHE 220>.A<CD1 9> and .R<PHE 220>.A<CE1 11>
WARNING: There is a bond of 20.132399 angstroms between:
------- .R<SER 222>.A<C 10> and .R<SER 222>.A<O 11>
WARNING: There is a bond of 20.146228 angstroms between:
------- .R<SER 222>.A<C 10> and .R<ILE 223>.A<N 1>
WARNING: There is a bond of 20.143205 angstroms between:
------- .R<SER 222>.A<CB 5> and .R<SER 222>.A<OG 8>
WARNING: There is a bond of 20.722135 angstroms between:
------- .R<SER 222>.A<CA 3> and .R<SER 222>.A<CB 5>
WARNING: There is a bond of 20.005051 angstroms between:
------- .R<ILE 223>.A<C 18> and .R<ILE 223>.A<O 19>
WARNING: There is a bond of 19.554786 angstroms between:
------- .R<ILE 223>.A<CA 3> and .R<ILE 223>.A<C 18>
WARNING: There is a bond of 20.933268 angstroms between:
------- .R<VAL 225>.A<C 15> and .R<PHE 226>.A<N 1>
WARNING: There is a bond of 19.450270 angstroms between:
------- .R<ASN 237>.A<C 13> and .R<ASN 237>.A<O 14>
WARNING: There is a bond of 19.893495 angstroms between:
------- .R<ILE 238>.A<C 18> and .R<CYS 239>.A<N 1>
WARNING: There is a bond of 19.211867 angstroms between:
------- .R<HIE 287>.A<C 16> and .R<HIE 287>.A<O 17>
WARNING: There is a bond of 18.871768 angstroms between:
------- .R<HIE 287>.A<CA 3> and .R<HIE 287>.A<CB 5>
WARNING: There is a bond of 21.176645 angstroms between:
------- .R<LYS 288>.A<CB 5> and .R<LYS 288>.A<CG 8>
WARNING: There is a bond of 19.439746 angstroms between:
------- .R<PHE 302>.A<C 19> and .R<PHE 302>.A<O 20>
WARNING: There is a bond of 19.851588 angstroms between:
------- .R<ILE 303>.A<C 18> and .R<PHE 304>.A<N 1>
WARNING: There is a bond of 19.243497 angstroms between:
------- .R<ILE 303>.A<CA 3> and .R<ILE 303>.A<C 18>
WARNING: There is a bond of 20.270792 angstroms between:
------- .R<PHE 304>.A<CA 3> and .R<PHE 304>.A<CB 5>
WARNING: There is a bond of 20.282716 angstroms between:
------- .R<PHE 304>.A<N 1> and .R<PHE 304>.A<CA 3>
WARNING: There is a bond of 19.402320 angstroms between:
------- .R<MET 371>.A<CA 3> and .R<MET 371>.A<C 16>
WARNING: There is a bond of 19.343980 angstroms between:
------- .R<LYS 378>.A<N 1> and .R<LYS 378>.A<CA 3>
WARNING: There is a bond of 21.078747 angstroms between:
------- .R<LYS 379>.A<CA 3> and .R<LYS 379>.A<C 21>
WARNING: There is a bond of 20.057094 angstroms between:
------- .R<LYS 390>.A<CB 5> and .R<LYS 390>.A<CG 8>
WARNING: There is a bond of 19.535055 angstroms between:
------- .R<CTYR 399>.A<CE2 16> and .R<CTYR 399>.A<CD2 18>
WARNING: There is a bond of 19.705675 angstroms between:
------- .R<CTYR 399>.A<CG 8> and .R<CTYR 399>.A<CD2 18>
WARNING: There is a bond of 19.856401 angstroms between:
------- .R<CTYR 399>.A<CB 5> and .R<CTYR 399>.A<CG 8>
WARNING: There is a bond of 19.249097 angstroms between:
------- .R<HIE 402>.A<C 16> and .R<ARG 403>.A<N 1>
WARNING: There is a bond of 20.901105 angstroms between:
------- .R<HIE 402>.A<CA 3> and .R<HIE 402>.A<CB 5>
WARNING: There is a bond of 19.987579 angstroms between:
------- .R<HIE 402>.A<CA 3> and .R<HIE 402>.A<C 16>
WARNING: There is a bond of 20.405535 angstroms between:
------- .R<ARG 403>.A<CB 5> and .R<ARG 403>.A<CG 8>
WARNING: There is a bond of 20.131809 angstroms between:
------- .R<TRP 408>.A<C 23> and .R<THR 409>.A<N 1>
WARNING: There is a bond of 19.748906 angstroms between:
------- .R<TRP 408>.A<NE1 11> and .R<TRP 408>.A<CE2 13>
WARNING: There is a bond of 19.386414 angstroms between:
------- .R<TRP 408>.A<CG 8> and .R<TRP 408>.A<CD1 9>
WARNING: There is a bond of 20.115849 angstroms between:
------- .R<TRP 408>.A<CA 3> and .R<TRP 408>.A<CB 5>
WARNING: There is a bond of 20.991188 angstroms between:
------- .R<THR 409>.A<CB 5> and .R<THR 409>.A<CG2 7>
WARNING: There is a bond of 19.982748 angstroms between:
------- .R<PRO 411>.A<CG 5> and .R<PRO 411>.A<CB 8>
WARNING: There is a bond of 19.806896 angstroms between:
------- .R<PRO 411>.A<CD 2> and .R<PRO 411>.A<CG 5>
WARNING: There is a bond of 19.020003 angstroms between:
------- .R<ASN 426>.A<C 13> and .R<ASN 426>.A<O 14>
WARNING: There is a bond of 21.022285 angstroms between:
------- .R<ASN 426>.A<CB 5> and .R<ASN 426>.A<CG 8>
WARNING: There is a bond of 20.246243 angstroms between:
------- .R<ASN 426>.A<CA 3> and .R<ASN 426>.A<CB 5>
WARNING: There is a bond of 18.935037 angstroms between:
------- .R<ILE 427>.A<C 18> and .R<ASP 428>.A<N 1>
WARNING: There is a bond of 19.945490 angstroms between:
------- .R<TYR 432>.A<N 1> and .R<TYR 432>.A<CA 3>
WARNING: There is a bond of 20.154212 angstroms between:
------- .R<THR 433>.A<CA 3> and .R<THR 433>.A<CB 5>
WARNING: There is a bond of 19.380348 angstroms between:
------- .R<GLY 436>.A<C 6> and .R<SER 437>.A<N 1>
WARNING: There is a bond of 19.640287 angstroms between:
------- .R<ARG 440>.A<C 23> and .R<ASN 441>.A<N 1>
WARNING: There is a bond of 19.564918 angstroms between:
------- .R<ARG 440>.A<CD 11> and .R<ARG 440>.A<NE 14>
WARNING: There is a bond of 20.641507 angstroms between:
------- .R<ILE 443>.A<CB 5> and .R<ILE 443>.A<CG1 11>
WARNING: There is a bond of 20.727355 angstroms between:
------- .R<HEM 497>.A<CBD 65> and .R<HEM 497>.A<CGD 68>
WARNING: There is a bond of 20.299434 angstroms between:
------- .R<HEM 497>.A<CBA 62> and .R<HEM 497>.A<CGA 69>
WARNING: There is a bond of 20.402226 angstroms between:
------- .R<HEM 497>.A<C2D 12> and .R<HEM 497>.A<CMD 48>
WARNING: There is a bond of 20.016604 angstroms between:
------- .R<ERY 498>.A<C9 13> and .R<ERY 498>.A<O11 14>
WARNING: There is a bond of 19.819553 angstroms between:
------- .R<ERY 498>.A<C8 12> and .R<ERY 498>.A<C33 20>
WARNING: There is a bond of 19.311291 angstroms between:
------- .R<ERY 498>.A<C3 7> and .R<ERY 498>.A<O3 17>
WARNING: There is a bond of 20.035048 angstroms between:
------- .R<ERY 498>.A<C2 6> and .R<ERY 498>.A<C30 25>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1470 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
ACE 1
CARG 1
CPRO 1
CSER 1
CTYR 2
CYP 1
ERY 1
HEM 1
NALA 1
NGLN 1
NILE 1
NSER 1
WAT 15845
)
(no restraints)
>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
??Please consider the environment before printing this e-mail
------------------------------
Message: 11
Date: Thu, 9 Apr 2015 07:18:33 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] xleap Menu bar problems
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <D0F8C316-6E19-4443-8D84-CAF262B6EDB6.gmail.com>
Content-Type: text/plain; charset=us-ascii
> On Apr 8, 2015, at 9:21 PM, Pierre Bertin <bertinp71.gmail.com> wrote:
>
> Hi there,
>
> I am a new member of this community and I try to use AMBER14. I have a
> problem with xleap menu. When I click on menu items (Edit, File) the table
> opens and closes suddenly wihtout letting me to select a function from the
> table. I saw the same problem in the mailing list Archives and the solution
> was : "Num. Lock Off". I already have Num. Lock turned Off. I also tried to
> uninstall and install AMBER14 and I have the same problem.
Are you clicking and holding? Or just clicking? The menus are not, in my experience persistent (i.e., you have to hold the click the entire time you are selecting the menu, and once you let up on the click, whatever is under the mouse cursor will be selected).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 12
Date: Thu, 9 Apr 2015 07:24:30 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] larger bonds between protein atoms
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <5C30FAB5-0CD9-452D-AD88-40241EE0C271.gmail.com>
Content-Type: text/plain; charset=utf-8
> On Apr 9, 2015, at 7:15 AM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> Hi All,
> I have prepared prmtop and inpcrd files as discussed in a recent thread
> (can't find the link in the archive yet).
> But I am getting strange warnings from tleap that there are large bonds
> between atoms of the same residues (protein and ligand).
> I have checked the coordinates for a couple of them and this doesn't look
> to be the case.
> Can you please take a look and suggest me if these are due to bad pdb
> structure or some other error?
You would know your system better than we would. You are getting errors because some of the residues that are adjacent in sequence are 20+ angstroms apart from one another. However, tleap will always try to connect two adjacent amino acid residues (or nucleic acid residues) that are not separated by a TER card.
So if your protein has multiple chains, you need to make sure that there is a TER card after the last atom in each chain so that tleap doesn?t try to bond the two chains together.
If there *aren?t* multiple chains, then your PDB looks like it has gaps in the sequence that you might have to fill in with some homology modeling tool or other PDB massager (I think PDBFixer will do this for you: https://github.com/pandegroup/pdbfixer <https://github.com/pandegroup/pdbfixer>).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 13
Date: Thu, 9 Apr 2015 07:32:40 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] MMPBSA error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <E3B651A4-7199-47CF-99EC-8047FF088CF4.gmail.com>
Content-Type: text/plain; charset=utf-8
> On Apr 8, 2015, at 11:50 PM, Abhishek TYAGI <atyagiaa.connect.ust.hk> wrote:
>
> Hi,
>
>
> 1. Dan: "It seems like somehow your cpptraj was built with MPI but ended up not
> being named cpptraj.MPI. What were the exact steps you used to
> configure and build amber?"
>
>
> I have two files named as cpptraj in the amberhome/bin/
>
>
> [atyagiaa.login-0 bin]$ $AMBERHOME/bin/cpptraj.MPI
>
> CPPTRAJ: Trajectory Analysis. V14.25 MPI
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Running on 1 threads
>> exit
> TIME: Total execution time: 84634.6979 seconds.
>
>
> [atyagiaa.login-0 bin]$ $AMBERHOME/bin/cpptraj
>
> CPPTRAJ: Trajectory Analysis. V14.25 MPI
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Running on 1 threads
This is a problem. I was interpreting your error message backwards -- Dan?s advice was the one to listen to.
This output shows that serial cpptraj is actually the MPI-parallel version. This should never happen (and indeed, I?ve never seen it happen), so something you did must have made cpptraj point to the parallel version (did you copy cpptraj.MPI into cpptraj?).
The solution is to reinstall Amber in *serial*.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 14
Date: Thu, 9 Apr 2015 08:00:56 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] larger bonds between protein atoms
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20150409120056.GC65039.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Thu, Apr 09, 2015, Vaibhav Dixit wrote:
> But I am getting strange warnings from tleap that there are large bonds
> between atoms of the same residues (protein and ligand).
> I have checked the coordinates for a couple of them and this doesn't look
> to be the case.
> WARNING: There is a bond of 20.901524 angstroms between:
> ------- .R<CYS 58>.A<CB 5> and .R<CYS 58>.A<SG 8>
In addition to Jason's point about perhaps needing TER cards, note that many
of the warnings are about bonds between side-chain atoms in the same residue.
This is very unusal. Can you say exactly what you did to "check the
coordinates"? Be sure that the coordinates in the input pdb file are in
the correct columns (PDB format is column-specific). Try loading just a small
piece of the protein (e.g. just residues 58-59) to see if that helps to debug
the problem. Use ambpdb or savepdb to create a pdb file from Amber prmtop,
and examine that visually (i.e. the otuput pdb, *not* your input pdb file).
These are just suggestions. Learning how to debug problems with simulations
is a key task, since problems are sure to arise from time to time.
....dac
------------------------------
Message: 15
Date: Thu, 9 Apr 2015 08:16:41 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] MMPBSA error
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAAC0qOYv7-WcZUQKeL2KBPqBEfXJwDSbKmcS-7V8Tc_iEPb7Nw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Wed, Apr 8, 2015 at 9:50 PM, Abhishek TYAGI <atyagiaa.connect.ust.hk> wrote:
> [atyagiaa.login-0 bin]$ $AMBERHOME/bin/cpptraj
>
> CPPTRAJ: Trajectory Analysis. V14.25 MPI
That's what I suspected. This will make mmpbsa.py very unhappy.
>> then somehow the serial version of cpptraj was overwritten with
>> cpptraj.MPI. Please tell us the exact commands you used to configure
>> and compile your Amber install.
>
> I followed the user manual amber14 to install on cluster.
You really need to provide the *exact* process (and I mean verbatim)
for us to have any hope of figuring out how this happened, especially
since I don't think anyone has had this happen to them before (I know
it hasn't happened to me, and I compile Amber a lot!). For example,
here's exactly what I did to install a test version of Amber this
morning:
tar -jxf AmberTools14.tar.bz2
cd amber14
export AMBERHOME=`pwd`
./configure gnu
make -j4 install
Also any other relevant information you can provide (such as what
compiler version, what MPI library, etc etc) would be great. Thanks,
-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)
------------------------------
Message: 16
Date: Thu, 9 Apr 2015 15:19:25 +0100
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Subject: Re: [AMBER] larger bonds between protein atoms
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAO6-0Tnh0TrRykTbpEgBtKnveRNru0x4DGNZ4wMYbYr9RepKyg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
I realized that the protein structure was the problem.
After building the missing residues (schrodinger prime module) prmtop and
inpcrd were generated without errors.
The charge command on the unit gives a value of 0.005998. This is after
neutralizing with 3 Cl- ions.
Do you consider this value of charge negligible or this needs further
adjustment?
Thank you.
Cheers.
Vaibhav
On Thu, Apr 9, 2015 at 1:00 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Thu, Apr 09, 2015, Vaibhav Dixit wrote:
>
> > But I am getting strange warnings from tleap that there are large bonds
> > between atoms of the same residues (protein and ligand).
> > I have checked the coordinates for a couple of them and this doesn't look
> > to be the case.
>
> > WARNING: There is a bond of 20.901524 angstroms between:
> > ------- .R<CYS 58>.A<CB 5> and .R<CYS 58>.A<SG 8>
>
> In addition to Jason's point about perhaps needing TER cards, note that
> many
> of the warnings are about bonds between side-chain atoms in the same
> residue.
>
> This is very unusal. Can you say exactly what you did to "check the
> coordinates"? Be sure that the coordinates in the input pdb file are in
> the correct columns (PDB format is column-specific). Try loading just a
> small
> piece of the protein (e.g. just residues 58-59) to see if that helps to
> debug
> the problem. Use ambpdb or savepdb to create a pdb file from Amber prmtop,
> and examine that visually (i.e. the otuput pdb, *not* your input pdb file).
>
> These are just suggestions. Learning how to debug problems with
> simulations
> is a key task, since problems are sure to arise from time to time.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
??Please consider the environment before printing this e-mail
------------------------------
Message: 17
Date: Thu, 9 Apr 2015 17:39:15 +0300
From: "Sofia Vasilakaki" <svasilak.chem.uoa.gr>
Subject: [AMBER] Problem with MMPBSA.py.MPI for nmode
To: amber.ambermd.org
Message-ID:
<c3da1dca6dcbe6f70fb932a2d121c5c9.squirrel.webmail01.uoa.gr>
Content-Type: text/plain;charset=utf-8
Hello to everyone!
So, I am trying to run MMPBSA.py.MPI for nmode and the calculation for
_MMPBSA_complex_nm.out gets stack in minimazition. The error I receive in
progress . log (between endless lines of Line minimizer aborted ...) is
Line minimizer aborted: max number of iterations reached
Line minimizer aborted: rounding error
Second derivatives are not supported for periodic systems; exiting.
File "/opt/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
app.run_mmpbsa()
File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /opt/amber14/bin/mmpbsa_py_nabnmode failed with prmtop Com.prmtop!
Error occured on rank 3.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
Line minimizer aborted: max number of iterations reached
I have try many different ways of setting up the process (such as: use
same protein but different ligands in amber12 & amber 14, gb=0 or 1, ways
of producing prmtops ... ) but always the same error. So, should I try
mm_pbsa instead? Has to do with the protein ? With the system ? Any other
ways for estimating entropy ?
Thank you in advance,
Sofia V.
------------------------------
Message: 18
Date: Thu, 9 Apr 2015 11:19:19 -0400
From: Kenneth Huang <kennethneltharion.gmail.com>
Subject: Re: [AMBER] Problem with MMPBSA.py.MPI for nmode
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CALeh7kDqaUWFzyznjj4aseMy6afku=uHfjet_K3W-yaJzXr4qA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Sofia,
Line minimizer aborted: max number of iterations reached
I think this might be your primary issue. I'm assuming that the error
message means the same thing as it would in other programs, so in this case
it'd mean that MMPBSA is hitting the maximum number of times it can try to
use- reading through the manual, I'd venture to guess that maxcyc is the
value you'd want to look at increasing?
As a good way to double check, have you checked what the mdout file says?
Though, I've never seen this error before in relation to Amber, and have
very limited experience with nmode, so someone else might want to weigh in.
Best,
Kenneth
On Thu, Apr 9, 2015 at 10:39 AM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
wrote:
> Hello to everyone!
>
> So, I am trying to run MMPBSA.py.MPI for nmode and the calculation for
> _MMPBSA_complex_nm.out gets stack in minimazition. The error I receive in
> progress . log (between endless lines of Line minimizer aborted ...) is
>
> Line minimizer aborted: max number of iterations reached
> Line minimizer aborted: rounding error
> Second derivatives are not supported for periodic systems; exiting.
> File "/opt/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
> app.run_mmpbsa()
> File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
> Calculation.run(self, rank, stdout=self.output % rank)
> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
> self.prmtop))
> CalcError: /opt/amber14/bin/mmpbsa_py_nabnmode failed with prmtop
> Com.prmtop!
> Error occured on rank 3.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
> Line minimizer aborted: max number of iterations reached
>
>
> I have try many different ways of setting up the process (such as: use
> same protein but different ligands in amber12 & amber 14, gb=0 or 1, ways
> of producing prmtops ... ) but always the same error. So, should I try
> mm_pbsa instead? Has to do with the protein ? With the system ? Any other
> ways for estimating entropy ?
>
> Thank you in advance,
> Sofia V.
>
>
> _______________________________________________
> 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: 19
Date: Thu, 9 Apr 2015 19:07:56 +0300
From: "Sofia Vasilakaki" <svasilak.chem.uoa.gr>
Subject: Re: [AMBER] Problem with MMPBSA.py.MPI for nmode
To: "AMBER Mailing List" <amber.ambermd.org>
Message-ID:
<36b3c79d684723d3dc1cb041e2758e2f.squirrel.webmail01.uoa.gr>
Content-Type: text/plain;charset=utf-8
Hi again,
So yes, I had increased maxcyc to 15000 without any difference ...
The _MMPBSA_complex_nm.out files have endless steps of min like the one
that follows. It is trying to do "something" but since I do not know how
mpbsa_entropy.nab works (could not understand the script either) I can not
figure out what is looking for or what cause the min process to fail.
MIN: Iter = 1011 NFunc = 8109 E = -20202.40567 RMSG = 3.0950510e-03
CG: It= 5 ( 0.404)q :-)
LS: i= 1 lhs_f= -0.00064243311 rhs_f= -1.4486479e-07
lhs_g= 0.00013928903 rhs_g= 0.0013037831
rel_s= 1 abs_s= 0.0091621209
max_d= 0.0022346375 i_xyz= 1321z
LS: step= 1 it= 1
MIN: Iter = 1012 NFunc = 8115 E = -20202.40633 RMSG = 2.4451938e-03
CG: It= 50 ( 3.946)q :-(
LS: i= 1 lhs_f= 0.090179125 rhs_f= -2.5904682e-06
lhs_g= 0.28272781 rhs_g= 0.023314214
rel_s= 1 abs_s= 0.490173
max_d= 0.11656831 i_xyz= 1321z
LS: i= 2 lhs_f= -0.0022555352 rhs_f= -4.10196e-07
lhs_g= 0.0012501516 rhs_g= 0.023314214
rel_s= 0.15834821 abs_s= 0.077618017
max_d= 0.018458384 i_xyz= 1321z
LS: step= 0.15834821 it= 2
> Sofia,
>
> Line minimizer aborted: max number of iterations reached
>
>
> I think this might be your primary issue. I'm assuming that the error
> message means the same thing as it would in other programs, so in this
> case
> it'd mean that MMPBSA is hitting the maximum number of times it can try to
> use- reading through the manual, I'd venture to guess that maxcyc is the
> value you'd want to look at increasing?
>
> As a good way to double check, have you checked what the mdout file says?
>
> Though, I've never seen this error before in relation to Amber, and have
> very limited experience with nmode, so someone else might want to weigh
> in.
>
> Best,
>
> Kenneth
>
> On Thu, Apr 9, 2015 at 10:39 AM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
> wrote:
>
>> Hello to everyone!
>>
>> So, I am trying to run MMPBSA.py.MPI for nmode and the calculation for
>> _MMPBSA_complex_nm.out gets stack in minimazition. The error I receive
>> in
>> progress . log (between endless lines of Line minimizer aborted ...) is
>>
>> Line minimizer aborted: max number of iterations reached
>> Line minimizer aborted: rounding error
>> Second derivatives are not supported for periodic systems; exiting.
>> File "/opt/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
>> app.run_mmpbsa()
>> File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
>> self.calc_list.run(rank, self.stdout)
>> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
>> calc.run(rank, stdout=stdout, stderr=stderr)
>> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 309, in run
>> Calculation.run(self, rank, stdout=self.output % rank)
>> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
>> self.prmtop))
>> CalcError: /opt/amber14/bin/mmpbsa_py_nabnmode failed with prmtop
>> Com.prmtop!
>> Error occured on rank 3.
>> Exiting. All files have been retained.
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
>> Line minimizer aborted: max number of iterations reached
>>
>>
>> I have try many different ways of setting up the process (such as: use
>> same protein but different ligands in amber12 & amber 14, gb=0 or 1,
>> ways
>> of producing prmtops ... ) but always the same error. So, should I try
>> mm_pbsa instead? Has to do with the protein ? With the system ? Any
>> other
>> ways for estimating entropy ?
>>
>> Thank you in advance,
>> Sofia V.
>>
>>
>> _______________________________________________
>> 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?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 20
Date: Thu, 9 Apr 2015 10:16:08 -0600
From: Pierre Bertin <bertinp71.gmail.com>
Subject: Re: [AMBER] xleap Menu bar problems
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAO3z7FLZr_CM0M8qQ4trHL6WjL1YghNM8__GXveiUKjhQidT5Q.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Jason,
that is right, menus are not persistent.
Thanks a lot for your answer, I saw it few minutes before! ;)
2015-04-09 5:18 GMT-06:00 Jason Swails <jason.swails.gmail.com>:
>
> > On Apr 8, 2015, at 9:21 PM, Pierre Bertin <bertinp71.gmail.com> wrote:
> >
> > Hi there,
> >
> > I am a new member of this community and I try to use AMBER14. I have a
> > problem with xleap menu. When I click on menu items (Edit, File) the
> table
> > opens and closes suddenly wihtout letting me to select a function from
> the
> > table. I saw the same problem in the mailing list Archives and the
> solution
> > was : "Num. Lock Off". I already have Num. Lock turned Off. I also tried
> to
> > uninstall and install AMBER14 and I have the same problem.
>
> Are you clicking and holding? Or just clicking? The menus are not, in my
> experience persistent (i.e., you have to hold the click the entire time you
> are selecting the menu, and once you let up on the click, whatever is under
> the mouse cursor will be selected).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
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Received on Thu Apr 09 2015 - 21:30:02 PDT