Dear Kuzmich and David;
Many thanks for your answers. In fact Python error was solved by Dr.
David's suggestion by logout and re-login to system. For Cuda problem, In
first instance I installed Opensuse15.0 (GCC7.x) with cuda9.2 driver
version 396.x. During make step for '-cuda' keyword I got many waning
messages but no error. I tried to replace Cuda9.2 with Cuda9.1 keeping
driver version 396.x but it gives me error at configure time that Cuda9.1
not work with GCC7.x. I changed my OS from Opensuse15.0 (GCC7.x) to
Opensuse42.3 (GCC4.8). I installed Cuda9.2 with driver version 396.x, I
again got many vague warning messages but no error. I, then, changed my
Cuda version from Cuda9.2 to Cuda9.1 keeping same driver i.e. nvidia driver
version 396.x. I got no vague warnings and installed Amber18 easily.
Following is type of the warning message that I got
" ptxas /tmp/tmpxft_00006011_00000000-5_kCalculateGBNonbondEnergy1.compute_61.ptx,
line* 4963*; warning : Instruction *'shfl*' without '.sync' is deprecated
since PTX ISA version 6.0 and will be discontinued in a future PTX ISA
version"
For compilation of each cuda-command, compiler threw many warning messages
like above on the terminal. The words in '*bold*' are changed with each
compilation step. With Cuda9.2, I got no error but only vague warning
messages and make step always completes without error. I have problem that
why I am getting so many vague warnings which do not pop-out with Cuda-9.1.
It makes me confuse that whether pmemd.cuda would be reliable or not.
One more thing, as Opensuse42.3 has GCC4.8, Cuda9.2 still gives vague
warning messages like above and Cuda9.1 do not give any vague warning
message like above. Now, it makes me think that it may not be a problem of
GCC7.x and / or Opensuse15.0, but of Cuda9.2 toolkit.
Regards;
On 26 July 2018 at 03:00, <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
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>
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> When replying, please edit your Subject line so it is more specific
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>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: calculating headgroup ion-ion and ion-dipole contacts for
> lipid bilayers (Wesley Michael Botello-Smith)
> 2. Re: LJEDIT syntax (Matias Machado)
> 3. Re: LJEDIT syntax (Matias Machado)
> 4. Re: Is Amber18 compatible with GCC-7.x (Nikolay N. Kuzmich)
> 5. Re: Is Amber18 compatible with GCC-7.x? (David A Case)
> 6. Re: Query regarding multiplication of LJ parameters by a
> constant in topology file using parmed (David A Case)
> 7. Re: LJEDIT syntax (David Cerutti)
> 8. problem preparing n-terminus with tleap (?) (Julia Belk)
> 9. Re: problem preparing n-terminus with tleap (?) (Matias Machado)
> 10. Problem in chamber (Suzan Bose)
> 11. Re: Query regarding multiplication of LJ parameters by a
> constant in topology file using parmed (Leena Aggarwal)
> 12. Re: Soft-core alchemical transformation in TI (Simon Kit Sang Chu)
> 13. Reading grid data from standard datafile (I L?rincz)
> 14. Re: Reading grid data from standard datafile (Daniel Roe)
> 15. Re: Soft-core alchemical transformation in TI
> (accuratefreeenergy.gmail.com)
> 16. Re: Soft-core alchemical transformation in TI (Simon Kit Sang Chu)
> 17. Re: Soft-core alchemical transformation in TI (Simon Kit Sang Chu)
> 18. Re: Soft-core alchemical transformation in TI
> (accuratefreeenergy.gmail.com)
> 19. MCBP force constants (Seibold, Steve Allan)
> 20. Re: Question about implicit solvation: DNA-linker conjugate
> (Supriyo Bhattacharya)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Jul 2018 12:06:54 -0700
> From: Wesley Michael Botello-Smith <wmsmith.uci.edu>
> Subject: Re: [AMBER] calculating headgroup ion-ion and ion-dipole
> contacts for lipid bilayers
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAMoQph_tt=52RbG4bQQPz=xSQz24QbpBfEkdyPwdsWbR2MmauA.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Here is what I did to compute average HBond distance data for use in a
> network analysis project recently.
> I did this using jupyter notebook, so I have pasted the commands from each
> cell I ran below.
> It should work as is provided you update the variables in the second block
> of commands to point to your trajectory and topology files.
>
> #Load needed packages
> import pytraj as pt
> import numpy as np
> import pandas as pd
> import collections
> from collections import OrderedDict as od
> import sys
> import re
>
> ###UPDATE THIS BLOCK ACCORDINGLY###
> #Setup paths to trajectory(ies) and topology
> strucBaseDir='/home/wesley/work/igps_network_analysis/
> Analysis/structures/aligned_trajectories/Apo/'
> trajDir=strucBaseDir+"/rep_1"
> topFileName="step3_charmm2amber.psf"
> trajFileName="all_production.aligned.dcd"
> topFilePath=strucBaseDir+"/"+topFileName
> trajFilePath=trajDir+"/"+trajFileName
> iterTraj=pt.iterload(trajFilePath,top=topFilePath)
> iterTraj
> ### ### ###
>
> #compute hbond for loaded trajectory
> #You can update this to match your system
> #It is essentiall just a wrapper for the equivalent cpptraj command
> hbond_data=pt.compute('hbond :1-454 dist 4.0 printatomnum
> series',iterTraj,n_cores=4)
> print hbond_data.keys()[1]
> print hbond_data[hbond_data.keys()[1]]
>
> #Find hbonds that existed for at least 1 frame...
> hbList=[]
> hbFreqs=[]
> nEntries=len(hbond_data.keys())
> print 'computing hbond frequencies |',
> for iKey in np.arange(nEntries):
> if iKey > 0:
> if iKey%np.floor(nEntries/10)==0:
> print '.',
> sys.stdout.flush()
>
> hbFreq=np.sum(hbond_data[hbond_data.keys()[iKey]])*1.0/iterTraj.n_frames
> if hbFreq>0: #can set higher frequency threshold if desired
> hbList.append(hbond_data.keys()[iKey])
> hbFreqs.append(hbFreq)
> print '|'
> print 'Number of hbonds detected: '+str(len(hbList))
> print hbList[0:9]
> print hbFreqs[0:9]
>
> #Use list of hbonds with non-zero frequency to compile a list
> #of distance commands to be run
> distCommands=[]
> for hbString in hbList:
> hbMasks=re.sub("[A-Z]*_",":",hbString).split("-")
> distCommand="distance "+hbMasks[0]+" "+hbMasks[1]
> distCommands.append(distCommand)
> distCommands[0:5]
>
> #Run the distance commands
> dist_data=pt.compute(distCommands,iterTraj,n_cores=4)
> print dist_data.keys()[0]+" = "+hbList[0]+" : ",
> print dist_data[dist_data.keys()[0]]
>
> #Compute average distances and compile into a pandas.DataFrame
> #then export as an ascii data table (or csv format if desired)
> averageDistances=pd.DataFrame({"HBond":hbList})
> tempList=[]
> for iKey in np.arange(len(hbList)):
> tempList.append(np.mean(dist_data[dist_data.keys()[iKey]]))
> averageDistances['Mean_Distance']=tempList
> print averageDistances.head()
> averageDistances.to_csv("average_hbond_distances.dat",sep=" ",index=False)
>
> On Tue, Jul 24, 2018 at 10:16 AM, Sally Pias <sallypias.gmail.com> wrote:
>
> > Hi Dan, Wesley, and Hai -
> >
> > Thank you all for your suggestions. The hbond command detected
> > charge-dipole interactions between phosphate O acceptors and O-H or N-H
> > donors. Nativecontacts also helped find headgroup phosphate-choline
> > interactions
> > -- achieved by setting mask1 and mask2 to the phosphate P and the choline
> > N. One other functionality that would be useful to me would be to record
> > the distance between atoms in the interactions detected. I want to know
> the
> > average headgroup-headgroup and headgroup-organic molecule interaction
> > distance in different bilayers.
> >
> > Best,
> > Sally
> >
> > --
> > Sally Pias
> > Assistant Professor of Chemistry
> > Faculty Adjunct, Department of Biology
> > New Mexico Tech
> > (575) 835-6204
> > www.nmt.edu/~spias
> > spias.nmt.edu
> >
> > On Fri, Jul 20, 2018 at 6:01 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > Just for clarity: pytraj works because it is cpptraj under the hood.
> > >
> > > Hai
> > >
> > > On Fri, Jul 20, 2018 at 7:57 PM Wesley Michael Botello-Smith <
> > > wmsmith.uci.edu> wrote:
> > >
> > > > nativecontacts works... pytraj can do this as well. If you want to
> > ensure
> > > > it is for ion to ion or ion to dipole, you can accomplish this using
> > > > appropriate selection masks. I think, if you use the convert the
> > contact
> > > > map into a matrix, you can use that to compute aggregate cluster
> sizes.
> > > >
> > > > On Fri, Jul 13, 2018, 3:19 PM Sally Pias <sallypias.gmail.com>
> wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I am looking for a way to count contacts between phospholipid
> > > headgroups
> > > > > and organic-lipid conjugate molecules embedded in a bilayer. Is
> > there a
> > > > > script or command similar to hbond that can calculate charge-charge
> > and
> > > > > ion-dipole contacts between nonsolvent residues (i.e., not water or
> > > > > monatomic ions)? Aggregate contact counts, as well as number of
> > > contacts
> > > > > over time would both be useful. Ideally, we need to be able to
> > identify
> > > > the
> > > > > residues and atoms involved.
> > > > >
> > > > > Thanks,
> > > > > Sally
> > > > >
> > > > > --
> > > > > Sally Pias
> > > > > Associate Professor of Chemistry
> > > > > Faculty Adjunct, Department of Biology
> > > > > New Mexico Tech
> > > > > _______________________________________________
> > > > > 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 24 Jul 2018 17:58:15 -0300 (UYT)
> From: Matias Machado <mmachado.pasteur.edu.uy>
> Subject: Re: [AMBER] LJEDIT syntax
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <2a8ca73a-764f-4357-b368-b06f55df2d8b.free.ipmont.lan>
> Content-Type: text/plain; charset=utf-8
>
> Thanks David,
>
> With your comments I was able to implement the special LJ parameters into
> the frcmod file.
>
> However, I notice that the actual parameters read for each atom type are
> "Rm/2" (= Rmh, "Rm half") and "epsilon" (e), same as in the NONBON section.
>
> So sigma_ij = (Rmh[type1] + Rmh[type2])*2^(1/6) and e_ij = sqrt(e[type1] *
> e[type2])
>
> The other important thing is that the section LJEDIT only affects the
> defined interaction (it doesn't overwrite the NONBON section). Indeed these
> three definitions of the A-B interaction render the same prmtop despite
> being different from a conceptual point of view:
>
> LJEDIT
> # type1 type1 Rmh[type1] e[type1] Rmh[type2] e[type2]
> A B 1.5 0.2 1.5 0.2
> A B 3.0 0.2 0.0 0.2
> A B 1.0 0.1 2.0 0.4
>
> By the way, I think this is a very nice feature that introduces a lot of
> flexibility to AMBER (comparable to other popular MD engines), I hope it
> won't be deprecated...
>
> Best,
>
> Mat?as
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "David Cerutti" <dscerutti.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 23 de Julio 2018 16:09:38
> Asunto: Re: [AMBER] LJEDIT syntax
>
> I'm the culprit here. I came up with that when we thought we needed
> parameters off the usual combining matrix. What the numbers stand for is
> the Lennard-Jones sigma and epsilon of the first atom type when it
> interacts with anything under the normal rules, then the sigma and epsilon
> of the second atom type when it interacts with the first. So all of those
> OW's in the parm14ipq.dat file have the sigma and epsilon of TIP4P-Ew water
> oxygen (the OW parameters are recast from the TIP3P which I sloppily left
> in the list above--TIP4P-Ew is the water model of choice for ff14ipq).
> Then, when type ND interacts with OW, it does so as if the ND has sigma and
> epsilon 2^(5/6) * 1.960000 A and 0.170000 kcal/mol. So the interaction of
> ND and OW takes place according to
>
> sigma = 0.5 * (1.775931 + 1.960000) * 2^(5/6) = 3.3283A
> epsilon = sqrt(0.162750 * 0.170000) = 0.16634 kcal/mol
>
> That's the way LJEDIT works. I'll see about getting this into the manual,
> but it's rare that someone has wanted the feature.
>
> Dave
>
>
>
> On Mon, Jul 23, 2018 at 2:16 PM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Dear AMBER experts,
> >
> > I'm trying to set some Lennard-Jones interactions out-off the combination
> > rule. I was able to do it by using Parmed, however I want to set them in
> a
> > frcmod file so they can be applied by leap without further modification
> of
> > the topology.
> >
> > I know the LJEDIT section (available from amber14 on) would allow me to
> do
> > so, however its syntax is poorly documented, indeed I couldn't find any
> > mention to that keyword in the Amber manuals, nor in the file formats at
> > the AMBER web page [http://ambermd.org/FileFormats.php]
> >
> > The only reference I found was this post in the mailing list [
> > http://dev-archive.ambermd.org/201301/0018.html], in which its
> > implementation is discussed. From those comments, I would expect the
> > following syntax:
> >
> > LJEDIT
> > <Type 1> <Type 2> <R* pair> <Eps pair>
> > ...
> > END
> >
> > However, looking at the implementation of parm14ipq.dat [
> > https://www.ncbi.nlm.nih.gov/pubmed/25328495] and CUFIX
> > (frcmod.ff99cufix) [http://bionano.physics.illinois.edu/CUFIX]
> > I found 4 terms instead of 2 for defining the LJ interaction, my guess is
> > that 1-4 interactions can also be set separately but I'm not sure about
> > that...
> >
> > In any case... what does each set of parameters stand for?
> >
> > Best regards,
> >
> > Mat?as
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/laboratorios-eng/lsbm]
> > [http://www.sirahff.com]
> >
> > _______________________________________________
> > 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: 3
> Date: Tue, 24 Jul 2018 18:01:45 -0300 (UYT)
> From: Matias Machado <mmachado.pasteur.edu.uy>
> Subject: Re: [AMBER] LJEDIT syntax
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <ffa77b8a-28f1-4ea0-870e-18da90bd7e65.free.ipmont.lan>
> Content-Type: text/plain; charset=utf-8
>
> Sorry about the typo...
>
> sigma_ij = (Rmh[type1] + Rmh[type2])*2^(-1/6)
>
> Matias
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Martes, 24 de Julio 2018 17:58:15
> Asunto: Re: [AMBER] LJEDIT syntax
>
> Thanks David,
>
> With your comments I was able to implement the special LJ parameters into
> the frcmod file.
>
> However, I notice that the actual parameters read for each atom type are
> "Rm/2" (= Rmh, "Rm half") and "epsilon" (e), same as in the NONBON section.
>
> So sigma_ij = (Rmh[type1] + Rmh[type2])*2^(1/6) and e_ij = sqrt(e[type1] *
> e[type2])
>
> The other important thing is that the section LJEDIT only affects the
> defined interaction (it doesn't overwrite the NONBON section). Indeed these
> three definitions of the A-B interaction render the same prmtop despite
> being different from a conceptual point of view:
>
> LJEDIT
> # type1 type1 Rmh[type1] e[type1] Rmh[type2] e[type2]
> A B 1.5 0.2 1.5 0.2
> A B 3.0 0.2 0.0 0.2
> A B 1.0 0.1 2.0 0.4
>
> By the way, I think this is a very nice feature that introduces a lot of
> flexibility to AMBER (comparable to other popular MD engines), I hope it
> won't be deprecated...
>
> Best,
>
> Mat?as
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "David Cerutti" <dscerutti.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 23 de Julio 2018 16:09:38
> Asunto: Re: [AMBER] LJEDIT syntax
>
> I'm the culprit here. I came up with that when we thought we needed
> parameters off the usual combining matrix. What the numbers stand for is
> the Lennard-Jones sigma and epsilon of the first atom type when it
> interacts with anything under the normal rules, then the sigma and epsilon
> of the second atom type when it interacts with the first. So all of those
> OW's in the parm14ipq.dat file have the sigma and epsilon of TIP4P-Ew water
> oxygen (the OW parameters are recast from the TIP3P which I sloppily left
> in the list above--TIP4P-Ew is the water model of choice for ff14ipq).
> Then, when type ND interacts with OW, it does so as if the ND has sigma and
> epsilon 2^(5/6) * 1.960000 A and 0.170000 kcal/mol. So the interaction of
> ND and OW takes place according to
>
> sigma = 0.5 * (1.775931 + 1.960000) * 2^(5/6) = 3.3283A
> epsilon = sqrt(0.162750 * 0.170000) = 0.16634 kcal/mol
>
> That's the way LJEDIT works. I'll see about getting this into the manual,
> but it's rare that someone has wanted the feature.
>
> Dave
>
>
>
> On Mon, Jul 23, 2018 at 2:16 PM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Dear AMBER experts,
> >
> > I'm trying to set some Lennard-Jones interactions out-off the combination
> > rule. I was able to do it by using Parmed, however I want to set them in
> a
> > frcmod file so they can be applied by leap without further modification
> of
> > the topology.
> >
> > I know the LJEDIT section (available from amber14 on) would allow me to
> do
> > so, however its syntax is poorly documented, indeed I couldn't find any
> > mention to that keyword in the Amber manuals, nor in the file formats at
> > the AMBER web page [http://ambermd.org/FileFormats.php]
> >
> > The only reference I found was this post in the mailing list [
> > http://dev-archive.ambermd.org/201301/0018.html], in which its
> > implementation is discussed. From those comments, I would expect the
> > following syntax:
> >
> > LJEDIT
> > <Type 1> <Type 2> <R* pair> <Eps pair>
> > ...
> > END
> >
> > However, looking at the implementation of parm14ipq.dat [
> > https://www.ncbi.nlm.nih.gov/pubmed/25328495] and CUFIX
> > (frcmod.ff99cufix) [http://bionano.physics.illinois.edu/CUFIX]
> > I found 4 terms instead of 2 for defining the LJ interaction, my guess is
> > that 1-4 interactions can also be set separately but I'm not sure about
> > that...
> >
> > In any case... what does each set of parameters stand for?
> >
> > Best regards,
> >
> > Mat?as
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/laboratorios-eng/lsbm]
> > [http://www.sirahff.com]
> >
> > _______________________________________________
> > 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: Wed, 25 Jul 2018 00:41:19 +0300
> From: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>
> Subject: Re: [AMBER] Is Amber18 compatible with GCC-7.x
> To: amber.ambermd.org
> Message-ID:
> <CAN0UxwDbj1LEpZpSiHm4De8yyCYgMep=k_CCb5-iQJqYkPSoRA.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Mirza and the Amber users,
>
> I have gcc 7.3.1 20180323 [gcc-7-branch revision 258812] compiler on my
> desktop
> with OpenSuse 15 and Amber18/CUDA 9.2 installed.
> This combination works well with GeForce GTX 970 and 1080Ti cards.
> At the beginning the CUDA drivers installation attempts (9.2, 9.1 and 9.0,
> the runfiles) were unsuccessful but the DKMS installation really solved it.
>
> Kind regards,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 24 Jul 2018 19:26:28 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Is Amber18 compatible with GCC-7.x?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20180724232628.s4unbern6dntjsz3.slater.local>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Jul 24, 2018, Ross Walker wrote:
>
> > > I have GTX 1050Ti GPU card, I installed graphics driver
> > > version 390.77, as CUDA9.2 have graphics driver version 396.x so I
> have to
> > > switch back to CUDA9.1 for CUDA compatibility with graphics driver
> version.
>
> Are you sure you need driver 390.77? (For other applications, maybe)?
> I have a GTX 1080 which is fine with cuda9.2, driver 296.26 and gcc
> 7.3.0.
>
> If things are working with an older version of opensuse, then you
> probably should just stick with that. But we *are* trying to support
> gcc7, and I don't yet know why my system works and yours does not. But
> I am using the driver that comes with cuda9.2, and perhaps that is not
> an option for you(?)
>
> ...regards
>
> p.s.: I hope going to the earlier OS also solved your python problems,
> which are unrelated to the cuda ones.
>
> .....dac
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 24 Jul 2018 19:28:52 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Query regarding multiplication of LJ parameters
> by a constant in topology file using parmed
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20180724232852.4qm37fo5ului4hfv.slater.local>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Jul 24, 2018, Leena Aggarwal wrote:
>
> >
> > Can we multiply the existing Lennard Jones parameters of the topology
> file
> > by a constant using parmed ??
>
> Changing epsilon will multiply an existing LJ term by the ratio of the new
> to the old epsilon value. Maybe that will do what you want?
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 24 Jul 2018 20:05:22 -0400
> From: David Cerutti <dscerutti.gmail.com>
> Subject: Re: [AMBER] LJEDIT syntax
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEmzWj2_69L1Yp=w0-912_0xBSK1Lxw470BdEQG2rhjW1S4bXA.
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Yes, that's correct. The sigma-related parameters are given with those
> multipliers to feed into a simplified equation (old Fortran codes reducing
> math operations).
>
> On Tue, Jul 24, 2018 at 5:02 PM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Sorry about the typo...
> >
> > sigma_ij = (Rmh[type1] + Rmh[type2])*2^(-1/6)
> >
> > Matias
> >
> > ----- Mensaje original -----
> > De: "Matias Machado" <mmachado.pasteur.edu.uy>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Martes, 24 de Julio 2018 17:58:15
> > Asunto: Re: [AMBER] LJEDIT syntax
> >
> > Thanks David,
> >
> > With your comments I was able to implement the special LJ parameters into
> > the frcmod file.
> >
> > However, I notice that the actual parameters read for each atom type are
> > "Rm/2" (= Rmh, "Rm half") and "epsilon" (e), same as in the NONBON
> section.
> >
> > So sigma_ij = (Rmh[type1] + Rmh[type2])*2^(1/6) and e_ij = sqrt(e[type1]
> *
> > e[type2])
> >
> > The other important thing is that the section LJEDIT only affects the
> > defined interaction (it doesn't overwrite the NONBON section). Indeed
> these
> > three definitions of the A-B interaction render the same prmtop despite
> > being different from a conceptual point of view:
> >
> > LJEDIT
> > # type1 type1 Rmh[type1] e[type1] Rmh[type2] e[type2]
> > A B 1.5 0.2 1.5 0.2
> > A B 3.0 0.2 0.0 0.2
> > A B 1.0 0.1 2.0 0.4
> >
> > By the way, I think this is a very nice feature that introduces a lot of
> > flexibility to AMBER (comparable to other popular MD engines), I hope it
> > won't be deprecated...
> >
> > Best,
> >
> > Mat?as
> >
> > ------------------------------------
> > PhD.
> > Researcher at Biomolecular Simulations Lab.
> > Institut Pasteur de Montevideo | Uruguay
> > [http://pasteur.uy/en/laboratorios-eng/lsbm]
> > [http://www.sirahff.com]
> >
> > ----- Mensaje original -----
> > De: "David Cerutti" <dscerutti.gmail.com>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Lunes, 23 de Julio 2018 16:09:38
> > Asunto: Re: [AMBER] LJEDIT syntax
> >
> > I'm the culprit here. I came up with that when we thought we needed
> > parameters off the usual combining matrix. What the numbers stand for is
> > the Lennard-Jones sigma and epsilon of the first atom type when it
> > interacts with anything under the normal rules, then the sigma and
> epsilon
> > of the second atom type when it interacts with the first. So all of
> those
> > OW's in the parm14ipq.dat file have the sigma and epsilon of TIP4P-Ew
> water
> > oxygen (the OW parameters are recast from the TIP3P which I sloppily left
> > in the list above--TIP4P-Ew is the water model of choice for ff14ipq).
> > Then, when type ND interacts with OW, it does so as if the ND has sigma
> and
> > epsilon 2^(5/6) * 1.960000 A and 0.170000 kcal/mol. So the interaction
> of
> > ND and OW takes place according to
> >
> > sigma = 0.5 * (1.775931 + 1.960000) * 2^(5/6) = 3.3283A
> > epsilon = sqrt(0.162750 * 0.170000) = 0.16634 kcal/mol
> >
> > That's the way LJEDIT works. I'll see about getting this into the
> manual,
> > but it's rare that someone has wanted the feature.
> >
> > Dave
> >
> >
> >
> > On Mon, Jul 23, 2018 at 2:16 PM Matias Machado <mmachado.pasteur.edu.uy>
> > wrote:
> >
> > > Dear AMBER experts,
> > >
> > > I'm trying to set some Lennard-Jones interactions out-off the
> combination
> > > rule. I was able to do it by using Parmed, however I want to set them
> in
> > a
> > > frcmod file so they can be applied by leap without further modification
> > of
> > > the topology.
> > >
> > > I know the LJEDIT section (available from amber14 on) would allow me to
> > do
> > > so, however its syntax is poorly documented, indeed I couldn't find any
> > > mention to that keyword in the Amber manuals, nor in the file formats
> at
> > > the AMBER web page [http://ambermd.org/FileFormats.php]
> > >
> > > The only reference I found was this post in the mailing list [
> > > http://dev-archive.ambermd.org/201301/0018.html], in which its
> > > implementation is discussed. From those comments, I would expect the
> > > following syntax:
> > >
> > > LJEDIT
> > > <Type 1> <Type 2> <R* pair> <Eps pair>
> > > ...
> > > END
> > >
> > > However, looking at the implementation of parm14ipq.dat [
> > > https://www.ncbi.nlm.nih.gov/pubmed/25328495] and CUFIX
> > > (frcmod.ff99cufix) [http://bionano.physics.illinois.edu/CUFIX]
> > > I found 4 terms instead of 2 for defining the LJ interaction, my guess
> is
> > > that 1-4 interactions can also be set separately but I'm not sure about
> > > that...
> > >
> > > In any case... what does each set of parameters stand for?
> > >
> > > Best regards,
> > >
> > > Mat?as
> > >
> > > ------------------------------------
> > > PhD.
> > > Researcher at Biomolecular Simulations Lab.
> > > Institut Pasteur de Montevideo | Uruguay
> > > [http://pasteur.uy/en/laboratorios-eng/lsbm]
> > > [http://www.sirahff.com]
> > >
> > > _______________________________________________
> > > 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: 8
> Date: Tue, 24 Jul 2018 18:32:26 -0700
> From: Julia Belk <jbelk.stanford.edu>
> Subject: [AMBER] problem preparing n-terminus with tleap (?)
> To: amber.ambermd.org
> Message-ID:
> <CANMhn3Qsx550Lq5j3u1aeqLZ5D4xo5GSvkprPxA4gsOyyfuDVg.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> I am not sure if this is a problem or not, but I'm slightly confused --
>
> I am trying to use tleap to prepare some structures, and it seems like
> charges are getting assigned differently to the n terminus and the c
> terminus.
>
> After loading and then saving a pdb file, the oxygen at the c terminus is
> given type OXT and, when I open the structure in maestro, has a formal
> charge of -1. However, the nitrogen at the n terminus is given type N, is
> bonded to CH3, but is not given a formal charge of +1.
>
> I don't have much experience with this, but I'm worried that if these
> charges aren't assigned correctly it might mess up my simulation, and I
> think that that nitrogen should be charged.
>
> Is there a way I can manually fix this? Or is it not a problem?
>
> Thanks,
> Julia
>
> PS - here is an example of the exact commands I'm running:
>
> 1. download pdb file (e.g., 3QDJ (look at the peptide -- chain C))
> 2. open tleap and run
>
> > source leaprc.protein.ff14SB
>
> > source leaprc.water.tip3p
>
> > mol = loadpdb 3QDJ.pdb
>
> > savepdb mol 3qdj_out.pdb
>
> 3. open 3qdj_out.pdb in maestro and inspect peptide termini
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 25 Jul 2018 00:07:18 -0300 (UYT)
> From: Matias Machado <mmachado.pasteur.edu.uy>
> Subject: Re: [AMBER] problem preparing n-terminus with tleap (?)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <c51589e2-70c0-4c57-880e-04bcc746a3d8.free.ipmont.lan>
> Content-Type: text/plain; charset=utf-8
>
> Dear Julia,
>
> Leap doesn't print the charges in the PDB file (like in a PQR file) so
> what you are seeing in maestro is due to the way maestro interprets the
> structure and not the actual parameters used in the AMBER force field
> (ff14SB). So, parameters are correctly set in the topology (.prmtop file)
> for the simulation with AMBER... If you have any doubt you can use xleap to
> visually inspect the atom charges assigned to the structure.
>
> Notice that by default N- and C- terminal residues are treated as
> zwitterionic, which means Leap will protonate the amine terminal and will
> generate a carboxy terminal by adding an extra oxygen atom (named OXT,
> please don't confuse the name with the type). I've never used maestro, but
> I guess that may be the reason for assigning a formal charge of -1 to OXT...
>
> Best,
>
> Mat?as
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Julia Belk" <jbelk.stanford.edu>
> Para: amber.ambermd.org
> Enviados: Martes, 24 de Julio 2018 22:32:26
> Asunto: [AMBER] problem preparing n-terminus with tleap (?)
>
> Hi all,
>
> I am not sure if this is a problem or not, but I'm slightly confused --
>
> I am trying to use tleap to prepare some structures, and it seems like
> charges are getting assigned differently to the n terminus and the c
> terminus.
>
> After loading and then saving a pdb file, the oxygen at the c terminus is
> given type OXT and, when I open the structure in maestro, has a formal
> charge of -1. However, the nitrogen at the n terminus is given type N, is
> bonded to CH3, but is not given a formal charge of +1.
>
> I don't have much experience with this, but I'm worried that if these
> charges aren't assigned correctly it might mess up my simulation, and I
> think that that nitrogen should be charged.
>
> Is there a way I can manually fix this? Or is it not a problem?
>
> Thanks,
> Julia
>
> PS - here is an example of the exact commands I'm running:
>
> 1. download pdb file (e.g., 3QDJ (look at the peptide -- chain C))
> 2. open tleap and run
>
> > source leaprc.protein.ff14SB
>
> > source leaprc.water.tip3p
>
> > mol = loadpdb 3QDJ.pdb
>
> > savepdb mol 3qdj_out.pdb
>
> 3. open 3qdj_out.pdb in maestro and inspect peptide termini
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 25 Jul 2018 09:40:45 +0530
> From: Suzan Bose <bosesuzan143.gmail.com>
> Subject: [AMBER] Problem in chamber
> To: amber.ambermd.org
> Message-ID:
> <CAEass7OOYPXvgVAzPBRzeWaU=7FbbPS66j9Kj4TFt4LeG=-ayA.
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
> I am a beginner of this amber field. I have installed amber16. I want to
> convert my charmm force field to amber format by the chamber module which
> is incorporated into the parmed, but unable to do. The error is as follows:
> ###################################################################
> ParmEd: a Parameter file Editor
> Reading input from STDIN...
> > chamber -top top_all22_prot.rtf -param par_all22_prot.prm -str
> toppar_water_ions.str -psf A.psf -crd A.pdb
> Creating chamber topology file from PSF A.psf, RTF files
> [top_all22_prot.rtf], PAR files [par_all22_prot.prm], and STR files
> [toppar_water_ions.str]. Coords from A.pdb. Using CMAP. GB Radius set
> mbondi.
> Unexpected failure:
> TypeError: 'str' object does not support item assignment
>
> Traceback is
>
> File
> "/data/apps/amber16/lib/python2.7/site-packages/
> parmed/tools/parmed_cmd.py",
> line 159, in _normaldo
> action.execute()
> File
> "/data/apps/amber16/lib/python2.7/site-packages/parmed/tools/actions.py",
> line 3883, in execute
> parmset.read_parameter_file(pfile)
> File
> "/data/apps/amber16/lib/python2.7/site-packages/
> parmed/charmm/parameters.py",
> line 415, in read_parameter_file
> elem = elem.lower(); elem[0] = elem[0].upper()
> #########################################################################
>
> Help me to get rid of this problem.
> Any comments/suggestions will be appreciated.
>
> Thanks,
> Suzan
>
>
> ------------------------------
>
> Message: 11
> Date: Wed, 25 Jul 2018 10:06:27 +0530
> From: Leena Aggarwal <leena.hrc.gmail.com>
> Subject: Re: [AMBER] Query regarding multiplication of LJ parameters
> by a constant in topology file using parmed
> To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOpqvR0r5SM_OzgNJhXf=3ijqZrmqf2LNSRH8DpEcdoJm5vyKA.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Amber Users
>
> I want to use coupling parameters (say 'a' and 'b') in the Kirkwood
> charging formula to scale the Lennard Jones parameters (a* sigma) and
> (b*charge) so, I want to multiply the constant 'a' with all sigma values in
> the topology file.
>
> On Wed, Jul 25, 2018 at 4:58 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Tue, Jul 24, 2018, Leena Aggarwal wrote:
> >
> > >
> > > Can we multiply the existing Lennard Jones parameters of the topology
> > file
> > > by a constant using parmed ??
> >
> > Changing epsilon will multiply an existing LJ term by the ratio of the
> new
> > to the old epsilon value. Maybe that will do what you want?
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 12
> Date: Wed, 25 Jul 2018 16:58:32 +0800
> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPqeSj=xw_b2h9fG5Z_fH44xFVTVeEJ+mYHj0Ua88H_
> iZJe5QA.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Taisung and Dave,
>
> I read the tiMerge command and its usage in page 429 of the manual. I
> notice it is feeding a single topology file ti.prmtop instead of two.
>
> To run parmed:
> >
> > parmed -p ti.prmtop -i merge.in
> >
> >
> >
> > The input for parmed (merge.in) looks like this:
> >
> > loadRestrt ti.inpcrd set
> >
> > Overwrite True
> >
> > tiMerge :1-5 :6-10 :3 :8
> >
> > outparm ti_merged.prmtop ti_merged.inpcrd
> >
> > quit
> >
> >
> In my case of methanol and ethanol, I do not have a merged topology file
> yet. How should I merge the restart files and individual topologies?
>
> Thanks!
> Simon
>
> <accuratefreeenergy.gmail.com> ? 2018?7?24??? ??8:50???
>
> > Hi Simon,
> >
> > Here are our answers:
> >
> > >So, I only have to set the timask and scmask on the atoms as in the
> > tutorial? All atoms present in timask while not in scmask
> > >will be transformed without soft-core potential automatically?
> >
> > Yes. All atoms in timask but not in scmask will be treated as
> > common atoms, provided that each common atom can find its partner atom
> and
> > all common atom pairs have the same coordinates (up to 0.1 A tolerance).
> >
> > >Second, I already simulated methanol solvated without the topology of
> > ethanol. If I want to keep the coordinate and *velocity*
> > >for a new TI, how should I prepare the files? The tutorial is preparing
> > benzene and phenol from a pdb file.
> > >Can I skip it by giving a rst file with coordinate and velocity
> > information?
> >
> > You could do that but not just directly using a methanol restart
> > file. The restart file only contains methanol coordinates. You need a
> > restart files containing both methanol and ethanol coordinates--although
> > they could be the same. You might use the tiMerge utility (manual page
> > 275) in the ParmED module (manual page 252) to merge a methanol restart
> > file w/ an ethanol restart file. It takes some time to learn how to use
> it
> > but it will be very useful if you want to TI/FEP/MBAR calculations often.
> >
> > Taisung & Dave
> >
> >
> > -----Original Message-----
> > From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> > Sent: Monday, July 23, 2018 10:44 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >
> > Dear David,
> >
> > Thanks for the info. I am also looked into the same tutorial. But I am
> > still confused to add soft-core potential atoms.
> >
> > According to AMBER16 manual, it seems that I do not have to add dummy
> > atoms for my case.
> >
> > > Note that a slightly different setup is required for using soft core
> > > potentials compared to older TI- implementations. Specifically, the
> > > difference is that to add or remove atoms without soft core
> > > potentials, they are transformed into interactionless dummy particles,
> > > so both end state prmtop files have the same number of atoms. When
> > > using soft core potentials instead, no dummy atoms are needed and the
> > > end states should be built without them.
> >
> >
> >
> > Thanks,
> > Simon
> >
> > David Cerutti <dscerutti.gmail.com> ? 2018?7?24??? ??12:57???
> >
> > > There are two ways to do it:
> > >
> > > 1.) Map the extra dummy atoms of ethanol to methanol: in this way,
> > > each atom has its exact mapped partner in methanol and ethanol, and
> > > they will have exactly the same coordinates. The masses of atoms do
> > > not affect the binding free energy so you don?t need to worry.
> > >
> > > 2.) Treat different atoms as ?softcore regions.? In this way, the
> > > different atoms will move independently.
> > >
> > > The second way is preferred, as the result will usually be much more
> > > stable.
> > >
> > > You can find the parameter settings in the manual (p426) and a
> > > step-by-step example in
> > http://ambermd.org/tutorials/advanced/tutorial9/index.html.
> > >
> > > Best of luck!
> > >
> > > Dave and Taisung
> > >
> > >
> > > On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
> > > simoncks1994.gmail.com>
> > > wrote:
> > >
> > > > Hi everyone,
> > > >
> > > > I am planning to transform a methanol into an ethanol. I did a
> > > > simulation of pure methanol solvated in water. I want to keep all
> > > > the coordinates
> > > and
> > > > velocities, including common hydrogens, in the restart in amber
> > > > format. I have two concerns right now.
> > > >
> > > > First, to transform from methanol to ethanol, I have to cut a
> > > > hydrogen
> > > out
> > > > from methanol and append a CH3- from the broken end. I briefly look
> > > > into AMBER manual and dummy atoms are necessary for pmemd
> > > > preparation. Atoms transformed must also have the same masses so I
> > > > cannot transform the hydrogen truncated into the new carbon. In that
> > > > case, how should the coordinate files be written? Can I skip
> > > > creating a pdb with a crd and include the hydrogens?
> > > >
> > > > Second, I am new to AMBER and I am not sure if it is using dual
> > topology.
> > > > If so, the CH3- will still be bonded with methanol while having no
> > > > LJ and electrostatics. However, will the thermal motion created by
> > > > the
> > > thermostat
> > > > alter the motion of methanol even at lambda = 0? If I am
> > > > transforming a methanol to a hexanol, the methanol motion would
> > > > largely be random due to the higher momentum of the "invisible"
> > (CH2)4-CH3 tail.
> > > >
> > > > I appreciate any advice. Sorry for the long mail!
> > > >
> > > > Regards,
> > > > Simon
> > > > _______________________________________________
> > > > 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 13
> Date: Wed, 25 Jul 2018 13:55:09 +0200
> From: I L?rincz <lorizoli.gmail.com>
> Subject: [AMBER] Reading grid data from standard datafile
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAC6C-8_YsL5_oqubuus8UDCaxp4Rb9kFbRffbxpwTj
> Xvc8mM_Q.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello!
>
> Exposition:
> I want to calculate the time averaged charge distribution in space of a
> certain part of a molecule. I used reference atoms in the rest of the
> molecule to remove translation/rotation and did the rms fit. I used volmap
> to calculate the density distribution of each atom in the interesting part
> and wrote the distributions out to standard data files with the following
> format:
> X Y Z D
> , where X,Y,Z are grid indexes and D is the prob density.
> I multiplied each distrbution with the corresponding atoms partial charge
> and summed them up, wrote them out to a Standard datafile of the same
> format (expecting to get the charge distribution from this process). Now I
> want to have a look at this. In order to do so I would need to read it back
> to ptraj and use grid with the pdb option to generate a pseudo-pdb file.
>
> Question starts here:
> I can't get ptraj to read or use a Standard datafile as a grid dataset. Is
> it possible? How do you create/define a grid dataset in ptraj?
>
> Thank for any help or wise words of wisdom,
> Istv?n L?rincz
>
>
> ------------------------------
>
> Message: 14
> Date: Wed, 25 Jul 2018 09:25:07 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Reading grid data from standard datafile
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOb5L7taDFCDxpLBq0=V0weUB_AhRvuvt0Q4mBG5uGgwyQ.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Oops - just took at look at the source code and sure enough the 3D
> standard data read function is empty. I think because I normally
> read/write 3D data in DX/Xplor/CCP4 format this just fell off of my
> radar. I've created an issue on GitHub
> (https://github.com/Amber-MD/cpptraj/issues/623) and will get to this
> as soon as I can.
>
> Sorry for the oversight!
>
> -Dan
>
> On Wed, Jul 25, 2018 at 7:55 AM, I L?rincz <lorizoli.gmail.com> wrote:
> > Hello!
> >
> > Exposition:
> > I want to calculate the time averaged charge distribution in space of a
> > certain part of a molecule. I used reference atoms in the rest of the
> > molecule to remove translation/rotation and did the rms fit. I used
> volmap
> > to calculate the density distribution of each atom in the interesting
> part
> > and wrote the distributions out to standard data files with the following
> > format:
> > X Y Z D
> > , where X,Y,Z are grid indexes and D is the prob density.
> > I multiplied each distrbution with the corresponding atoms partial charge
> > and summed them up, wrote them out to a Standard datafile of the same
> > format (expecting to get the charge distribution from this process). Now
> I
> > want to have a look at this. In order to do so I would need to read it
> back
> > to ptraj and use grid with the pdb option to generate a pseudo-pdb file.
> >
> > Question starts here:
> > I can't get ptraj to read or use a Standard datafile as a grid dataset.
> Is
> > it possible? How do you create/define a grid dataset in ptraj?
> >
> > Thank for any help or wise words of wisdom,
> > Istv?n L?rincz
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 15
> Date: Wed, 25 Jul 2018 12:10:48 -0400
> From: <accuratefreeenergy.gmail.com>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <000601d42432$0d59f130$280dd390$.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Simon,
>
> Here is what I usually do--other developers may have other better
> ways:
>
> 1. Create PDB files for your methanol and ethanol. You can use cpptraj to
> convert your coordinate/restart files into pdb files. Or if you only have
> ethanol--create one for it, make a copy, and change the residue names in
> the copied one so that it becomes a "methanol" pdb.
> 2. Merge your two PDB files into one by hand--at this stage, you also may
> modify the coordinates for each atom so that, for example, the common atoms
> have exactly the same coordinates.
> 3. Use tleap to read the combined PDB and produce the combined
> topology/crd files.
> 4. Use tiMerge to merge the common parts.
>
> Taisung
>
> -----Original Message-----
> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> Sent: Wednesday, July 25, 2018 4:59 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
>
> Dear Taisung and Dave,
>
> I read the tiMerge command and its usage in page 429 of the manual. I
> notice it is feeding a single topology file ti.prmtop instead of two.
>
> To run parmed:
> >
> > parmed -p ti.prmtop -i merge.in
> >
> >
> >
> > The input for parmed (merge.in) looks like this:
> >
> > loadRestrt ti.inpcrd set
> >
> > Overwrite True
> >
> > tiMerge :1-5 :6-10 :3 :8
> >
> > outparm ti_merged.prmtop ti_merged.inpcrd
> >
> > quit
> >
> >
> In my case of methanol and ethanol, I do not have a merged topology file
> yet. How should I merge the restart files and individual topologies?
>
> Thanks!
> Simon
>
> <accuratefreeenergy.gmail.com> ? 2018?7?24??? ??8:50???
>
> > Hi Simon,
> >
> > Here are our answers:
> >
> > >So, I only have to set the timask and scmask on the atoms as in the
> > tutorial? All atoms present in timask while not in scmask
> > >will be transformed without soft-core potential automatically?
> >
> > Yes. All atoms in timask but not in scmask will be treated as
> > common atoms, provided that each common atom can find its partner atom
> > and all common atom pairs have the same coordinates (up to 0.1 A
> tolerance).
> >
> > >Second, I already simulated methanol solvated without the topology of
> > ethanol. If I want to keep the coordinate and *velocity*
> > >for a new TI, how should I prepare the files? The tutorial is
> > >preparing
> > benzene and phenol from a pdb file.
> > >Can I skip it by giving a rst file with coordinate and velocity
> > information?
> >
> > You could do that but not just directly using a methanol
> > restart file. The restart file only contains methanol coordinates.
> > You need a restart files containing both methanol and ethanol
> > coordinates--although they could be the same. You might use the
> > tiMerge utility (manual page
> > 275) in the ParmED module (manual page 252) to merge a methanol
> > restart file w/ an ethanol restart file. It takes some time to learn
> > how to use it but it will be very useful if you want to TI/FEP/MBAR
> calculations often.
> >
> > Taisung & Dave
> >
> >
> > -----Original Message-----
> > From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> > Sent: Monday, July 23, 2018 10:44 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >
> > Dear David,
> >
> > Thanks for the info. I am also looked into the same tutorial. But I am
> > still confused to add soft-core potential atoms.
> >
> > According to AMBER16 manual, it seems that I do not have to add dummy
> > atoms for my case.
> >
> > > Note that a slightly different setup is required for using soft core
> > > potentials compared to older TI- implementations. Specifically, the
> > > difference is that to add or remove atoms without soft core
> > > potentials, they are transformed into interactionless dummy
> > > particles, so both end state prmtop files have the same number of
> > > atoms. When using soft core potentials instead, no dummy atoms are
> > > needed and the end states should be built without them.
> >
> >
> >
> > Thanks,
> > Simon
> >
> > David Cerutti <dscerutti.gmail.com> ? 2018?7?24??? ??12:57???
> >
> > > There are two ways to do it:
> > >
> > > 1.) Map the extra dummy atoms of ethanol to methanol: in this way,
> > > each atom has its exact mapped partner in methanol and ethanol, and
> > > they will have exactly the same coordinates. The masses of atoms do
> > > not affect the binding free energy so you don?t need to worry.
> > >
> > > 2.) Treat different atoms as ?softcore regions.? In this way, the
> > > different atoms will move independently.
> > >
> > > The second way is preferred, as the result will usually be much more
> > > stable.
> > >
> > > You can find the parameter settings in the manual (p426) and a
> > > step-by-step example in
> > http://ambermd.org/tutorials/advanced/tutorial9/index.html.
> > >
> > > Best of luck!
> > >
> > > Dave and Taisung
> > >
> > >
> > > On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
> > > simoncks1994.gmail.com>
> > > wrote:
> > >
> > > > Hi everyone,
> > > >
> > > > I am planning to transform a methanol into an ethanol. I did a
> > > > simulation of pure methanol solvated in water. I want to keep all
> > > > the coordinates
> > > and
> > > > velocities, including common hydrogens, in the restart in amber
> > > > format. I have two concerns right now.
> > > >
> > > > First, to transform from methanol to ethanol, I have to cut a
> > > > hydrogen
> > > out
> > > > from methanol and append a CH3- from the broken end. I briefly
> > > > look into AMBER manual and dummy atoms are necessary for pmemd
> > > > preparation. Atoms transformed must also have the same masses so I
> > > > cannot transform the hydrogen truncated into the new carbon. In
> > > > that case, how should the coordinate files be written? Can I skip
> > > > creating a pdb with a crd and include the hydrogens?
> > > >
> > > > Second, I am new to AMBER and I am not sure if it is using dual
> > topology.
> > > > If so, the CH3- will still be bonded with methanol while having no
> > > > LJ and electrostatics. However, will the thermal motion created by
> > > > the
> > > thermostat
> > > > alter the motion of methanol even at lambda = 0? If I am
> > > > transforming a methanol to a hexanol, the methanol motion would
> > > > largely be random due to the higher momentum of the "invisible"
> > (CH2)4-CH3 tail.
> > > >
> > > > I appreciate any advice. Sorry for the long mail!
> > > >
> > > > Regards,
> > > > Simon
> > > > _______________________________________________
> > > > 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
> >
> >
> > _______________________________________________
> > 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: 16
> Date: Thu, 26 Jul 2018 00:17:52 +0800
> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPqeSjkuXN=iw2Z3zUH0d5_+066yBM8F+TrKKhszthwgvW5O3w.
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Taisung,
>
> So there seems to be no way to bypass pdb and manually merge them with the
> TER card even with inpcrd. If I am modifying the coordinates, I may not be
> able to restore all equilibrated atom coordinates.
>
> Please correct me if I am wrong.
>
> Regards,
> Simon
>
> <accuratefreeenergy.gmail.com> ? 2018?7?26??? ??12:11???
>
> > Hi Simon,
> >
> > Here is what I usually do--other developers may have other better
> > ways:
> >
> > 1. Create PDB files for your methanol and ethanol. You can use cpptraj
> to
> > convert your coordinate/restart files into pdb files. Or if you only
> have
> > ethanol--create one for it, make a copy, and change the residue names in
> > the copied one so that it becomes a "methanol" pdb.
> > 2. Merge your two PDB files into one by hand--at this stage, you also may
> > modify the coordinates for each atom so that, for example, the common
> atoms
> > have exactly the same coordinates.
> > 3. Use tleap to read the combined PDB and produce the combined
> > topology/crd files.
> > 4. Use tiMerge to merge the common parts.
> >
> > Taisung
> >
> > -----Original Message-----
> > From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> > Sent: Wednesday, July 25, 2018 4:59 AM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >
> > Dear Taisung and Dave,
> >
> > I read the tiMerge command and its usage in page 429 of the manual. I
> > notice it is feeding a single topology file ti.prmtop instead of two.
> >
> > To run parmed:
> > >
> > > parmed -p ti.prmtop -i merge.in
> > >
> > >
> > >
> > > The input for parmed (merge.in) looks like this:
> > >
> > > loadRestrt ti.inpcrd set
> > >
> > > Overwrite True
> > >
> > > tiMerge :1-5 :6-10 :3 :8
> > >
> > > outparm ti_merged.prmtop ti_merged.inpcrd
> > >
> > > quit
> > >
> > >
> > In my case of methanol and ethanol, I do not have a merged topology file
> > yet. How should I merge the restart files and individual topologies?
> >
> > Thanks!
> > Simon
> >
> > <accuratefreeenergy.gmail.com> ? 2018?7?24??? ??8:50???
> >
> > > Hi Simon,
> > >
> > > Here are our answers:
> > >
> > > >So, I only have to set the timask and scmask on the atoms as in the
> > > tutorial? All atoms present in timask while not in scmask
> > > >will be transformed without soft-core potential automatically?
> > >
> > > Yes. All atoms in timask but not in scmask will be treated as
> > > common atoms, provided that each common atom can find its partner atom
> > > and all common atom pairs have the same coordinates (up to 0.1 A
> > tolerance).
> > >
> > > >Second, I already simulated methanol solvated without the topology of
> > > ethanol. If I want to keep the coordinate and *velocity*
> > > >for a new TI, how should I prepare the files? The tutorial is
> > > >preparing
> > > benzene and phenol from a pdb file.
> > > >Can I skip it by giving a rst file with coordinate and velocity
> > > information?
> > >
> > > You could do that but not just directly using a methanol
> > > restart file. The restart file only contains methanol coordinates.
> > > You need a restart files containing both methanol and ethanol
> > > coordinates--although they could be the same. You might use the
> > > tiMerge utility (manual page
> > > 275) in the ParmED module (manual page 252) to merge a methanol
> > > restart file w/ an ethanol restart file. It takes some time to learn
> > > how to use it but it will be very useful if you want to TI/FEP/MBAR
> > calculations often.
> > >
> > > Taisung & Dave
> > >
> > >
> > > -----Original Message-----
> > > From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> > > Sent: Monday, July 23, 2018 10:44 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> > >
> > > Dear David,
> > >
> > > Thanks for the info. I am also looked into the same tutorial. But I am
> > > still confused to add soft-core potential atoms.
> > >
> > > According to AMBER16 manual, it seems that I do not have to add dummy
> > > atoms for my case.
> > >
> > > > Note that a slightly different setup is required for using soft core
> > > > potentials compared to older TI- implementations. Specifically, the
> > > > difference is that to add or remove atoms without soft core
> > > > potentials, they are transformed into interactionless dummy
> > > > particles, so both end state prmtop files have the same number of
> > > > atoms. When using soft core potentials instead, no dummy atoms are
> > > > needed and the end states should be built without them.
> > >
> > >
> > >
> > > Thanks,
> > > Simon
> > >
> > > David Cerutti <dscerutti.gmail.com> ? 2018?7?24??? ??12:57???
> > >
> > > > There are two ways to do it:
> > > >
> > > > 1.) Map the extra dummy atoms of ethanol to methanol: in this way,
> > > > each atom has its exact mapped partner in methanol and ethanol, and
> > > > they will have exactly the same coordinates. The masses of atoms do
> > > > not affect the binding free energy so you don?t need to worry.
> > > >
> > > > 2.) Treat different atoms as ?softcore regions.? In this way, the
> > > > different atoms will move independently.
> > > >
> > > > The second way is preferred, as the result will usually be much more
> > > > stable.
> > > >
> > > > You can find the parameter settings in the manual (p426) and a
> > > > step-by-step example in
> > > http://ambermd.org/tutorials/advanced/tutorial9/index.html.
> > > >
> > > > Best of luck!
> > > >
> > > > Dave and Taisung
> > > >
> > > >
> > > > On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
> > > > simoncks1994.gmail.com>
> > > > wrote:
> > > >
> > > > > Hi everyone,
> > > > >
> > > > > I am planning to transform a methanol into an ethanol. I did a
> > > > > simulation of pure methanol solvated in water. I want to keep all
> > > > > the coordinates
> > > > and
> > > > > velocities, including common hydrogens, in the restart in amber
> > > > > format. I have two concerns right now.
> > > > >
> > > > > First, to transform from methanol to ethanol, I have to cut a
> > > > > hydrogen
> > > > out
> > > > > from methanol and append a CH3- from the broken end. I briefly
> > > > > look into AMBER manual and dummy atoms are necessary for pmemd
> > > > > preparation. Atoms transformed must also have the same masses so I
> > > > > cannot transform the hydrogen truncated into the new carbon. In
> > > > > that case, how should the coordinate files be written? Can I skip
> > > > > creating a pdb with a crd and include the hydrogens?
> > > > >
> > > > > Second, I am new to AMBER and I am not sure if it is using dual
> > > topology.
> > > > > If so, the CH3- will still be bonded with methanol while having no
> > > > > LJ and electrostatics. However, will the thermal motion created by
> > > > > the
> > > > thermostat
> > > > > alter the motion of methanol even at lambda = 0? If I am
> > > > > transforming a methanol to a hexanol, the methanol motion would
> > > > > largely be random due to the higher momentum of the "invisible"
> > > (CH2)4-CH3 tail.
> > > > >
> > > > > I appreciate any advice. Sorry for the long mail!
> > > > >
> > > > > Regards,
> > > > > Simon
> > > > > _______________________________________________
> > > > > 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
> > >
> > >
> > > _______________________________________________
> > > 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: 17
> Date: Wed, 25 Jul 2018 16:21:36 +0800
> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPqeSjnLn2apg1RL4ZdAjFzR-E6aG010nBpQKHPGSAZv46fgRw.
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Sorry, one more thing to add. So even if I am using soft-core potential, I
> still have to match their coordinates? Specifically to my case, how should
> I map the atoms H in methanol to CH3 in ethanol? I am a bit confused.
>
> Thanks,
> Simon
>
> Simon Kit Sang Chu <simoncks1994.gmail.com> ? 2018?7?26??? ??12:17???
>
> > Hi Taisung,
> >
> > So there seems to be no way to bypass pdb and manually merge them with
> the
> > TER card even with inpcrd. If I am modifying the coordinates, I may not
> be
> > able to restore all equilibrated atom coordinates.
> >
> > Please correct me if I am wrong.
> >
> > Regards,
> > Simon
> >
> > <accuratefreeenergy.gmail.com> ? 2018?7?26??? ??12:11???
> >
> >> Hi Simon,
> >>
> >> Here is what I usually do--other developers may have other
> better
> >> ways:
> >>
> >> 1. Create PDB files for your methanol and ethanol. You can use cpptraj
> >> to convert your coordinate/restart files into pdb files. Or if you only
> >> have ethanol--create one for it, make a copy, and change the residue
> names
> >> in the copied one so that it becomes a "methanol" pdb.
> >> 2. Merge your two PDB files into one by hand--at this stage, you also
> may
> >> modify the coordinates for each atom so that, for example, the common
> atoms
> >> have exactly the same coordinates.
> >> 3. Use tleap to read the combined PDB and produce the combined
> >> topology/crd files.
> >> 4. Use tiMerge to merge the common parts.
> >>
> >> Taisung
> >>
> >> -----Original Message-----
> >> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> >> Sent: Wednesday, July 25, 2018 4:59 AM
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >>
> >> Dear Taisung and Dave,
> >>
> >> I read the tiMerge command and its usage in page 429 of the manual. I
> >> notice it is feeding a single topology file ti.prmtop instead of two.
> >>
> >> To run parmed:
> >> >
> >> > parmed -p ti.prmtop -i merge.in
> >> >
> >> >
> >> >
> >> > The input for parmed (merge.in) looks like this:
> >> >
> >> > loadRestrt ti.inpcrd set
> >> >
> >> > Overwrite True
> >> >
> >> > tiMerge :1-5 :6-10 :3 :8
> >> >
> >> > outparm ti_merged.prmtop ti_merged.inpcrd
> >> >
> >> > quit
> >> >
> >> >
> >> In my case of methanol and ethanol, I do not have a merged topology file
> >> yet. How should I merge the restart files and individual topologies?
> >>
> >> Thanks!
> >> Simon
> >>
> >> <accuratefreeenergy.gmail.com> ? 2018?7?24??? ??8:50???
> >>
> >> > Hi Simon,
> >> >
> >> > Here are our answers:
> >> >
> >> > >So, I only have to set the timask and scmask on the atoms as in the
> >> > tutorial? All atoms present in timask while not in scmask
> >> > >will be transformed without soft-core potential automatically?
> >> >
> >> > Yes. All atoms in timask but not in scmask will be treated as
> >> > common atoms, provided that each common atom can find its partner atom
> >> > and all common atom pairs have the same coordinates (up to 0.1 A
> >> tolerance).
> >> >
> >> > >Second, I already simulated methanol solvated without the topology of
> >> > ethanol. If I want to keep the coordinate and *velocity*
> >> > >for a new TI, how should I prepare the files? The tutorial is
> >> > >preparing
> >> > benzene and phenol from a pdb file.
> >> > >Can I skip it by giving a rst file with coordinate and velocity
> >> > information?
> >> >
> >> > You could do that but not just directly using a methanol
> >> > restart file. The restart file only contains methanol coordinates.
> >> > You need a restart files containing both methanol and ethanol
> >> > coordinates--although they could be the same. You might use the
> >> > tiMerge utility (manual page
> >> > 275) in the ParmED module (manual page 252) to merge a methanol
> >> > restart file w/ an ethanol restart file. It takes some time to learn
> >> > how to use it but it will be very useful if you want to TI/FEP/MBAR
> >> calculations often.
> >> >
> >> > Taisung & Dave
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> >> > Sent: Monday, July 23, 2018 10:44 PM
> >> > To: AMBER Mailing List <amber.ambermd.org>
> >> > Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >> >
> >> > Dear David,
> >> >
> >> > Thanks for the info. I am also looked into the same tutorial. But I am
> >> > still confused to add soft-core potential atoms.
> >> >
> >> > According to AMBER16 manual, it seems that I do not have to add dummy
> >> > atoms for my case.
> >> >
> >> > > Note that a slightly different setup is required for using soft core
> >> > > potentials compared to older TI- implementations. Specifically, the
> >> > > difference is that to add or remove atoms without soft core
> >> > > potentials, they are transformed into interactionless dummy
> >> > > particles, so both end state prmtop files have the same number of
> >> > > atoms. When using soft core potentials instead, no dummy atoms are
> >> > > needed and the end states should be built without them.
> >> >
> >> >
> >> >
> >> > Thanks,
> >> > Simon
> >> >
> >> > David Cerutti <dscerutti.gmail.com> ? 2018?7?24??? ??12:57???
> >> >
> >> > > There are two ways to do it:
> >> > >
> >> > > 1.) Map the extra dummy atoms of ethanol to methanol: in this way,
> >> > > each atom has its exact mapped partner in methanol and ethanol, and
> >> > > they will have exactly the same coordinates. The masses of atoms do
> >> > > not affect the binding free energy so you don?t need to worry.
> >> > >
> >> > > 2.) Treat different atoms as ?softcore regions.? In this way, the
> >> > > different atoms will move independently.
> >> > >
> >> > > The second way is preferred, as the result will usually be much more
> >> > > stable.
> >> > >
> >> > > You can find the parameter settings in the manual (p426) and a
> >> > > step-by-step example in
> >> > http://ambermd.org/tutorials/advanced/tutorial9/index.html.
> >> > >
> >> > > Best of luck!
> >> > >
> >> > > Dave and Taisung
> >> > >
> >> > >
> >> > > On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
> >> > > simoncks1994.gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Hi everyone,
> >> > > >
> >> > > > I am planning to transform a methanol into an ethanol. I did a
> >> > > > simulation of pure methanol solvated in water. I want to keep all
> >> > > > the coordinates
> >> > > and
> >> > > > velocities, including common hydrogens, in the restart in amber
> >> > > > format. I have two concerns right now.
> >> > > >
> >> > > > First, to transform from methanol to ethanol, I have to cut a
> >> > > > hydrogen
> >> > > out
> >> > > > from methanol and append a CH3- from the broken end. I briefly
> >> > > > look into AMBER manual and dummy atoms are necessary for pmemd
> >> > > > preparation. Atoms transformed must also have the same masses so I
> >> > > > cannot transform the hydrogen truncated into the new carbon. In
> >> > > > that case, how should the coordinate files be written? Can I skip
> >> > > > creating a pdb with a crd and include the hydrogens?
> >> > > >
> >> > > > Second, I am new to AMBER and I am not sure if it is using dual
> >> > topology.
> >> > > > If so, the CH3- will still be bonded with methanol while having no
> >> > > > LJ and electrostatics. However, will the thermal motion created by
> >> > > > the
> >> > > thermostat
> >> > > > alter the motion of methanol even at lambda = 0? If I am
> >> > > > transforming a methanol to a hexanol, the methanol motion would
> >> > > > largely be random due to the higher momentum of the "invisible"
> >> > (CH2)4-CH3 tail.
> >> > > >
> >> > > > I appreciate any advice. Sorry for the long mail!
> >> > > >
> >> > > > Regards,
> >> > > > Simon
> >> > > > _______________________________________________
> >> > > > 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
> >> >
> >> >
> >> > _______________________________________________
> >> > 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: Wed, 25 Jul 2018 12:37:30 -0400
> From: <accuratefreeenergy.gmail.com>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <000c01d42435$c81e42c0$585ac840$.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Simon,
>
> That's my understanding--maybe others have better ways.
>
> If you have both methanol and ethanol equilibrated, you only can
> use one, right?
>
> You need to match the common atoms--does that make sense? If your
> common atoms do not have the same coordinates, how can Amber handle them as
> common atoms?
>
> For SC atoms, they don't need to be matched. So you don't need to
> match H in methanol to CH3 in ethanol.
>
> For example, if you have only ethanol equilibrated, I would create a pdb
> for ethanol, make a copy of it, and in the copied pdb, change the residue
> name into methanol, delete H's in CH3, and change C into H--now the copy is
> a "methanol" pdb.
>
> Use tleap to merge this original ethanol with the modified "methanol"
> pdb. Create the combined topology and crd files.
>
> Then in tiMerge define -CH2-OH as common atoms, and CH3- (ethanol) and H-
> (methanol) as SC atoms.
>
>
> Taisung
>
> -----Original Message-----
> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> Sent: Wednesday, July 25, 2018 4:22 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
>
> Sorry, one more thing to add. So even if I am using soft-core potential, I
> still have to match their coordinates? Specifically to my case, how should
> I map the atoms H in methanol to CH3 in ethanol? I am a bit confused.
>
> Thanks,
> Simon
>
> Simon Kit Sang Chu <simoncks1994.gmail.com> ? 2018?7?26??? ??12:17???
>
> > Hi Taisung,
> >
> > So there seems to be no way to bypass pdb and manually merge them with
> > the TER card even with inpcrd. If I am modifying the coordinates, I
> > may not be able to restore all equilibrated atom coordinates.
> >
> > Please correct me if I am wrong.
> >
> > Regards,
> > Simon
> >
> > <accuratefreeenergy.gmail.com> ? 2018?7?26??? ??12:11???
> >
> >> Hi Simon,
> >>
> >> Here is what I usually do--other developers may have other
> >> better
> >> ways:
> >>
> >> 1. Create PDB files for your methanol and ethanol. You can use
> >> cpptraj to convert your coordinate/restart files into pdb files. Or
> >> if you only have ethanol--create one for it, make a copy, and change
> >> the residue names in the copied one so that it becomes a "methanol" pdb.
> >> 2. Merge your two PDB files into one by hand--at this stage, you also
> >> may modify the coordinates for each atom so that, for example, the
> >> common atoms have exactly the same coordinates.
> >> 3. Use tleap to read the combined PDB and produce the combined
> >> topology/crd files.
> >> 4. Use tiMerge to merge the common parts.
> >>
> >> Taisung
> >>
> >> -----Original Message-----
> >> From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> >> Sent: Wednesday, July 25, 2018 4:59 AM
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >>
> >> Dear Taisung and Dave,
> >>
> >> I read the tiMerge command and its usage in page 429 of the manual. I
> >> notice it is feeding a single topology file ti.prmtop instead of two.
> >>
> >> To run parmed:
> >> >
> >> > parmed -p ti.prmtop -i merge.in
> >> >
> >> >
> >> >
> >> > The input for parmed (merge.in) looks like this:
> >> >
> >> > loadRestrt ti.inpcrd set
> >> >
> >> > Overwrite True
> >> >
> >> > tiMerge :1-5 :6-10 :3 :8
> >> >
> >> > outparm ti_merged.prmtop ti_merged.inpcrd
> >> >
> >> > quit
> >> >
> >> >
> >> In my case of methanol and ethanol, I do not have a merged topology
> >> file yet. How should I merge the restart files and individual
> topologies?
> >>
> >> Thanks!
> >> Simon
> >>
> >> <accuratefreeenergy.gmail.com> ? 2018?7?24??? ??8:50???
> >>
> >> > Hi Simon,
> >> >
> >> > Here are our answers:
> >> >
> >> > >So, I only have to set the timask and scmask on the atoms as in
> >> > >the
> >> > tutorial? All atoms present in timask while not in scmask
> >> > >will be transformed without soft-core potential automatically?
> >> >
> >> > Yes. All atoms in timask but not in scmask will be treated
> >> > as common atoms, provided that each common atom can find its
> >> > partner atom and all common atom pairs have the same coordinates
> >> > (up to 0.1 A
> >> tolerance).
> >> >
> >> > >Second, I already simulated methanol solvated without the topology
> >> > >of
> >> > ethanol. If I want to keep the coordinate and *velocity*
> >> > >for a new TI, how should I prepare the files? The tutorial is
> >> > >preparing
> >> > benzene and phenol from a pdb file.
> >> > >Can I skip it by giving a rst file with coordinate and velocity
> >> > information?
> >> >
> >> > You could do that but not just directly using a methanol
> >> > restart file. The restart file only contains methanol coordinates.
> >> > You need a restart files containing both methanol and ethanol
> >> > coordinates--although they could be the same. You might use the
> >> > tiMerge utility (manual page
> >> > 275) in the ParmED module (manual page 252) to merge a methanol
> >> > restart file w/ an ethanol restart file. It takes some time to
> >> > learn how to use it but it will be very useful if you want to
> >> > TI/FEP/MBAR
> >> calculations often.
> >> >
> >> > Taisung & Dave
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: Simon Kit Sang Chu <simoncks1994.gmail.com>
> >> > Sent: Monday, July 23, 2018 10:44 PM
> >> > To: AMBER Mailing List <amber.ambermd.org>
> >> > Subject: Re: [AMBER] Soft-core alchemical transformation in TI
> >> >
> >> > Dear David,
> >> >
> >> > Thanks for the info. I am also looked into the same tutorial. But I
> >> > am still confused to add soft-core potential atoms.
> >> >
> >> > According to AMBER16 manual, it seems that I do not have to add
> >> > dummy atoms for my case.
> >> >
> >> > > Note that a slightly different setup is required for using soft
> >> > > core potentials compared to older TI- implementations.
> >> > > Specifically, the difference is that to add or remove atoms
> >> > > without soft core potentials, they are transformed into
> >> > > interactionless dummy particles, so both end state prmtop files
> >> > > have the same number of atoms. When using soft core potentials
> >> > > instead, no dummy atoms are needed and the end states should be
> built without them.
> >> >
> >> >
> >> >
> >> > Thanks,
> >> > Simon
> >> >
> >> > David Cerutti <dscerutti.gmail.com> ? 2018?7?24??? ??12:57???
> >> >
> >> > > There are two ways to do it:
> >> > >
> >> > > 1.) Map the extra dummy atoms of ethanol to methanol: in this
> >> > > way, each atom has its exact mapped partner in methanol and
> >> > > ethanol, and they will have exactly the same coordinates. The
> >> > > masses of atoms do not affect the binding free energy so you don?t
> need to worry.
> >> > >
> >> > > 2.) Treat different atoms as ?softcore regions.? In this way,
> >> > > the different atoms will move independently.
> >> > >
> >> > > The second way is preferred, as the result will usually be much
> >> > > more stable.
> >> > >
> >> > > You can find the parameter settings in the manual (p426) and a
> >> > > step-by-step example in
> >> > http://ambermd.org/tutorials/advanced/tutorial9/index.html.
> >> > >
> >> > > Best of luck!
> >> > >
> >> > > Dave and Taisung
> >> > >
> >> > >
> >> > > On Mon, Jul 23, 2018 at 11:12 AM Simon Kit Sang Chu <
> >> > > simoncks1994.gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Hi everyone,
> >> > > >
> >> > > > I am planning to transform a methanol into an ethanol. I did a
> >> > > > simulation of pure methanol solvated in water. I want to keep
> >> > > > all the coordinates
> >> > > and
> >> > > > velocities, including common hydrogens, in the restart in amber
> >> > > > format. I have two concerns right now.
> >> > > >
> >> > > > First, to transform from methanol to ethanol, I have to cut a
> >> > > > hydrogen
> >> > > out
> >> > > > from methanol and append a CH3- from the broken end. I briefly
> >> > > > look into AMBER manual and dummy atoms are necessary for pmemd
> >> > > > preparation. Atoms transformed must also have the same masses
> >> > > > so I cannot transform the hydrogen truncated into the new
> >> > > > carbon. In that case, how should the coordinate files be
> >> > > > written? Can I skip creating a pdb with a crd and include the
> hydrogens?
> >> > > >
> >> > > > Second, I am new to AMBER and I am not sure if it is using dual
> >> > topology.
> >> > > > If so, the CH3- will still be bonded with methanol while having
> >> > > > no LJ and electrostatics. However, will the thermal motion
> >> > > > created by the
> >> > > thermostat
> >> > > > alter the motion of methanol even at lambda = 0? If I am
> >> > > > transforming a methanol to a hexanol, the methanol motion would
> >> > > > largely be random due to the higher momentum of the "invisible"
> >> > (CH2)4-CH3 tail.
> >> > > >
> >> > > > I appreciate any advice. Sorry for the long mail!
> >> > > >
> >> > > > Regards,
> >> > > > Simon
> >> > > > _______________________________________________
> >> > > > 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
> >> >
> >> >
> >> > _______________________________________________
> >> > 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
> >>
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 19
> Date: Wed, 25 Jul 2018 17:23:02 +0000
> From: "Seibold, Steve Allan" <stevesei.ku.edu>
> Subject: [AMBER] MCBP force constants
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <1532539382340.96625.ku.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I am working my way through MCBP (not MCBP.py) tutorial. I have gotten to
> the point of
>
> "Gaussian based Side Chain Model Optimization and Frequency Calculation".
> At this point from my understanding I must select the method for force
> constant calculation..i.e. Z-matrix or the Seminario method...However, I
> don't understand how I am to select.?? Is this a method I select in
> Gaussian (I can't find it in G03)?
>
>
> Thanks, Steve
>
>
> ------------------------------
>
> Message: 20
> Date: Wed, 25 Jul 2018 17:32:20 +0000 (UTC)
> From: Supriyo Bhattacharya <sup27606.yahoo.com>
> Subject: Re: [AMBER] Question about implicit solvation: DNA-linker
> conjugate
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <163633408.2803003.1532539940741.mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Matias,Thank you for pointing me to parmed. I am going to check it
> out. Right now, I assigned the new residue one of the recognized nucleotide
> residue names. This allows Amber to recognize it as a nucleotide and assign
> the nucleotide GB parameters. This seems to have solved the problem for
> now, but I understand that it's an unclean solution. So, the proper way
> would be to provide the right parameters in the topology itself.
> As for suggesting the salt concentration, that was really helpful. This
> was not a problem for the protein simulations, but with DNA, setting the
> saltcon to 0.15 solved the issue of DNA unfolding. Now, the DNA structure
> is completely stable for 1 microsec and counting.
> Thanks so much for both the suggestions. You guys are a wonderful
> community!
> Supriyo
>
> On Tuesday, July 24, 2018, 7:44:06 AM PDT, Matias Machado <
> mmachado.pasteur.edu.uy> wrote:
>
> Dear Supriyo,
>
> You can modify the GB parameters in the topology with Parmed using the
> command "change RADII <mask> <new-value>" (check de manual)...
>
> By the way, are you setting the an ionic concentration while running with
> GBSA (e.g. saltcon=0.15)? That may be very important to avoid
> polyelectrolite melting as they are heavy charged molecules...
>
> Best,
>
> Mat?as
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Supriyo Bhattacharya" <sup27606.yahoo.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 23 de Julio 2018 17:53:50
> Asunto: Re: [AMBER] Question about implicit solvation: DNA-linker conjugate
>
> Hello Dr. Simmerling,Thank you for the reply. I would like to carefully
> assign the GB parameters myself, but I am looking for a way to provide the
> parameters in the leap input file or the run script without having to edit
> the source code. Is there a way to do this?
> Many thanks,Supriyo
>
> ? ? On Monday, July 23, 2018, 11:11:47 AM PDT, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:?
>
> Gb neck was only tested with proteins and nucleic acids, and the intrinsic
> Born radii are optimized for those. If you create a new molecule (such as
> your linker), you'll also want to carefully check the radii that leap
> assigns to those atoms. They may not be appropriate. You'll probably want
> to try to assign them by analogy rather than the guess leap takes.
>
> On Mon, Jul 23, 2018, 2:06 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > hi,
> >
> > which amber version you're using? (Just to make sure you have updated
> igb8
> > parameters for DNA/RNA in amber 17 or 18).
> >
> > By the way, 310K is pretty high in GB simulation (in my experience), you
> > can try with 300K.
> >
> > >? The same system when simulated in explicit water remains stable and
> does
> > not show aggregation of the phosphates.
> >
> > How long did you run? (implicit solvent has faster sampling, so you might
> > want to run much longer explicit water to compare).
> >
> > Hai
> >
> > On Sun, Jul 22, 2018 at 2:30 PM, Supriyo Bhattacharya <
> sup27606.yahoo.com>
> > wrote:
> >
> > > Hi everyone,I am trying to simulate the dynamics of a linker conjugated
> > > DNA strand using implicit solvation in AMBER. The formula of the
> > molecule I
> > > am trying to simulate is:
> > > 5'GGTGCATCGATGCAGGGGGG-L-L-L-L-L-C-A-T-T-T-C-C-C-G-T-A-A-A-T-C-L-L
> > >? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? |? ? |?
> |
> > >? |? |? |? |? |? |? ? |? |? |? |? |? |? ? ? |
> > >
> >? 3'-L-L-L-L-G-T-A-A-A-G-G-G-C-A-T-T-T-A-G-L-L
> > > , where L (linker) = -(PO4)-(CH2)-(CH2)-(CH2)-
> > > I have parameterized the linker using Antechamber and assigned am-bcc1
> > > charges. Next I edited the linker prepi file in xleap and specified the
> > > head and tail atoms. Finally, I created a frcmod file where I specified
> > the
> > > missing parameters (mostly the connections between L and nucleotides)
> > taken
> > > from the DNA.bsc1 parameter set. When I performed a test run using
> igb=8
> > at
> > > 310K, all the phosphate groups in the linker aggregated together
> > > immediately and destroyed the DNA double helix. The same system when
> > > simulated in explicit water remains stable and does not show
> aggregation
> > of
> > > the phosphates.
> > > Could someone with experience advise what is going wrong with the
> > implicit
> > > solvation. Do I need to set any other parameter for the linker
> phosphates
> > > specific to GB solvation (explicit water simulations work fine). Also,
> > the
> > > partial charges on the phosphate group are similar if not identical to
> > the
> > > DNA phosphates. The missing dihedral parameters for the linker were
> also
> > > taken from equivalent parameters in DNA. I am wondering whether the
> > alpha,
> > > beta and gamma parameters of IGB need to be explicitly set for the
> linker
> > > atoms. I thought some default reasonable values are already assigned by
> > > AMBER. Please note, I have some prior experience with GB solvent
> > > simulations in AMBER, although all of them were with pure protein
> > systems.
> > > Could somebody help?
> > > Many thanks in advance,Supriyo
> > > _______________________________________________
> > > 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
> ?
> _______________________________________________
> 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
>
>
> ------------------------------
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 2360, Issue 1
> **************************************
>
--
Mirza A. Hammad (Cell: +8613161676988)
PhD Scholar
Institute of Biophysics, UCAS
Beijing. China
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Received on Wed Jul 25 2018 - 20:30:03 PDT
