Re: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"

for -nstlist and -ntomp, as Szilard already mentioned). Best regards, Alan --- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use

Re: [gmx-users] question on dihedrals propers func 3 and impropers func 1

Which version of ACPYPE are you using? Please, get the latest here: https://github.com/alanwilter/acpype Check also about option: -z, --gmx4write RB dihedrals old GMX 4.0 Thanks for using ACPYPE! Alan On Sat, 1 Feb 2020 at 18:21, Lei Qian wrote: > Dear users, > > Coul

[gmx-users] New ACPYPE server

again. If don't know what ACPYPE is but you're a looking for a way to speed up the process of generating topologies for unusual small molecules like inhibitors, ligands or drugs? Then check it out. If having issues, please don't hesitate to let us know. Thanks! Alan, Luciano

Re: [gmx-users] acpype error

it to me, with your input file if you don't mind. Thanks for using ACPYPE. Best regards Alan On Wed, 10 Jul 2019 at 07:57, Mahboobeh Eslami wrote: > I installed acpype to generate the necessary files of ligand.if I use > this command: > "Acpype -i ligand.mol2 -c user"

Re: [gmx-users] About 2019 GMX manual

Dear Benson and Paul, Thank you both very much. I will open the issue in redmine and, Benson, I'd appreciate if you could act on my behalf at gerrit. Best regards, Alan On Mon, 8 Jul 2019 at 03:37, Paul bauer wrote: > Hello, > > as Benson said, please open an issue at redmine.g

[gmx-users] About 2019 GMX manual

Is there a better way to report issues with the current manual? It's a very minor one, to update a link about ACPYPE on page 25. To use: https://github.com/alanwilter/acpype Thanks, Alan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

[gmx-users] Spatially resolved diffusion coefficient

Dear GROMACS users, I am interested in obtaining a spatially resolved diffusion coefficient for water in a confined pore system consisting of a slab of metal and water. My goal is to obtain the xy component of diffusion coefficient (parallel to the metal slab) as a function of distance away fr

Re: [gmx-users] ACPYPE not working.

Ok, I'm still using Amber16, yours is 2018. I believe that they made FATAL error now the warning we used to have with 2016 version. There's nothing I can do. Please, seek Amber mailing list help. Alan On Fri, 2 Nov 2018 at 19:03, neelam wafa wrote: > Hi! > This is the command

Re: [gmx-users] ACPYPE not working.

Please, post here the command you're using (add -d anyway for debug) and show the whole output. Thanks, Alan On Thu, 1 Nov 2018 at 20:04, neelam wafa wrote: > Yes it the same one. And the tests are running okay. Problem is with my > files. > > On Fri, 2 Nov 2018, 12:56 am Ala

Re: [gmx-users] ACPYPE not working.

| On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > Means this file worked well on your system? > > On Fri, 2 Nov 2018, 12:38 am Alan > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to > get > &g

Re: [gmx-users] ACPYPE not working.

This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get help at AMBER mailing list. For an example I was given, running here: acpype -di H16.mol2 -c gas DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi mol2 -o tmp -fo ac -pf y DEBUG: Warning: the

Re: [gmx-users] acpype

Are you running python3? what python -V or python3 -V outputs? Alan On Mon, 29 Oct 2018 at 13:25, neelam wafa wrote: > Hi > Thanks for your help. I have resolved that problem but got another one . > when I run the command > > ../acpype.py -i FFF.pdb > > I g

Re: [gmx-users] acpype

n you have. Thanks, Alan On Thu, 25 Oct 2018 at 16:44, neelam wafa wrote: > Hi, Alan > > I have installed amber tools 18 for antechamber and acpype with > > git clone https://github.com/alanwilter/acpype.git > > then installed it with > ln -s $PWD/acpype.py /usr/local/bi

Re: [gmx-users] acpype

We are working on it now. I can't tell you exactly because we need several tests. It's a complete new version re-written from scratch. I'm really sorry for the inconvenience but we hope to bring it back in a month or two. Alan On Wed, 24 Oct 2018 at 16:58, neelam wafa wrote: &g

Re: [gmx-users] acpype

Indeed, it's mostly Luciano spearheading these new things. Hopefully, we will have more things to show eventually. Alan On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar < bhupendra.dandekar...@gmail.com> wrote: > I actually got lot of help from Luciano Kagami about installation

Re: [gmx-users] acpype

Thanks Bhupendra, indeed we have this option, which is experimental, but I'm glad to see some are already using it and it seems to be working. Alan On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar < bhupendra.dandekar...@gmail.com> wrote: > Dear Farial, > > Use this comma

Re: [gmx-users] acpype

ly if converting from Amber to GMX that you do not need Antechamber (but if you play with AMBER format, you certainly have AmberTools installed, right?) I hope it helps, Alan On Wed, 24 Oct 2018 at 09:31, Farial Tavakoli wrote: > Dear GMX useres > > I am trying to convert .OFF and .FRCMOD files

Re: [gmx-users] Location of latest version of Acpype

Please, see here https://github.com/alanwilter/acpype And many thanks for using ACPYPE! Alan On Tue, 23 Oct 2018 at 21:02, Matthew Fisher wrote: > Dear all, > > > I'm currently trying to locate the latest version of acpype and have been > unable to find a working link to

Re: [gmx-users] i have queston about partial charge zinc

one up and running but unfortunately I can predict a date for the return. For sure, we will announce in the proper channels when the new server is up. Sorry for the inconvenience, Alan On Sun, 30 Sep 2018 at 09:11, neelam wafa wrote: > Hi ! > Alan the link for updated acpype you have shared

Re: [gmx-users] i have queston about partial charge zinc

Please, official, original, updated ACPYPE is now here: https://github.com/alanwilter/acpype Alan On 20 September 2018 at 13:56, Andrea Coletta wrote: > In general I would say that +2 is not a good choice, since it seems to me > that this is a Zinc complex. > > You may want to

Re: [gmx-users] Output forces only for select group of atoms

-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, February 27, 2018 3:18 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Output forces only for select group of atoms On 2/27/18 6:16 PM, Jacob Alan Spooner wrote: > Hi Mark, > > Thank you for yo

Re: [gmx-users] Output forces only for select group of atoms

18 at 10:28 PM Jacob Alan Spooner wrote: > Dear GROMACS users, > > I am simulating a fairly large system of about 25 atoms and I want to > analyze the forces at each output step for only a select group of about 200 > atoms (and actually only the z component of the force but this

[gmx-users] Output forces only for select group of atoms

Dear GROMACS users, I am simulating a fairly large system of about 25 atoms and I want to analyze the forces at each output step for only a select group of about 200 atoms (and actually only the z component of the force but this is less important). My question is whether or not there is a

[gmx-users] Formula for 9-3 wall potential

Dear GROMACS users, I am attempting some simulations using the wall option with the 9-3 potential. The manual is very brief on this topic and does not explicitly show the form of this potential. If anybody is familiar enough with using the 9-3 walls, am I correct to assume the interaction bet

Re: [gmx-users] Conversion Amber to Gromacs

://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > >

Re: [gmx-users] Creating cyclic peptides

requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscrib

Re: [gmx-users] ligand topology

> GAFF is compatible with AMBER (by design). My comments were warning that > > one should not use AMBER for a protein in concert with GROMOS for a > ligand. > > > > -Justin > > > > Best regards. > >> Lucio Montero. > >> > >> Enviado

Re: [gmx-users] ligand topology

s Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit

Re: [gmx-users] REGARDING TOPOLOGY FILE

ve at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mai

[gmx-users] ACPYPE now works with GAFF2

Now one can do: acpype -a gaff2 -i ... See 'acpype -h' for more details: -a ATOM_TYPE, --atom_type=ATOM_TYPE atom type, can be gaff, gaff2, amber (AMBER14SB) or amber2 (AMBER14SB + GAFF2), default is gaff Thanks for using ACP

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

But read the GMX manual to understand why it's all fine. On 12 October 2016 at 13:29, Dd H wrote: > Thank you! > > On 12 October 2016 at 19:50, Alan wrote: > > > It's all fine. > > > > On 12 October 2016 at 12:34, Dd H wrote: > > > > >

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

It's all fine. On 12 October 2016 at 12:34, Dd H wrote: > I use this command: > acpype -p filename.prmtop -x filename.inpcrd > > It generates parameter files for GROMACS and my question is about the .top > file of outputs. > > On 12 October 2016 at 18:22, Alan wrote:

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

fo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Unit

Re: [gmx-users] Porting to Gromacs of Parmbsc1

energy minimization step the system blows up > (very likely is because of water molecules overlapping). > > Another approach I followed was to load everything on Amber and export to > Gromacs with ACPYPE before solvating and adding ions. Then I tried to > generate the box in gromacs but

Re: [gmx-users] top parameters for pluronic f127

ge for all internal units of your polymer and the extreme to model your terminals. Good luck, Alan On 3 June 2016 at 18:37, SAKO MIRZAIE wrote: > Dear All, > > I am trying to convert my mol2 file to amber99sb itp to do MD by > gromacs. but, when I use ACPYPE software, it run and nev

[gmx-users] Getting and keeping ACPYPE updated

Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- Gromacs Users mailing list * Please

Re: [gmx-users] updates about ACPYPE

trying to look at the Urey-Bradley potential but I can’t promise anything. It should still be compatible with GMX 4 and 5, but now parameters are generated to GMX 4.5/5 by default. I am not aware of any issue. Thanks, Alan On 22 October 2015 at 02:27, yunshi11 . wrote: > Hi Alan, > >

Re: [gmx-users] Virtual Sites in protein-ligand systems

/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > h

Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

On 27 October 2015 at 14:59, Mark Abraham wrote: > 3nm box Dear Mark, 3nm in gro file sorted my issue. I was pulling my hair putting 10 nm (>5 times the largest vector of my molecule) and it was not working. Many thanks! Alan -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinforma

Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

approach. So, which minimum parameters do I have to define to run an EM using steep-descent with 500 iters? Alan On 27 October 2015 at 13:38, Victor Rosas Garcia wrote: > As I understand it, this error is not dependent on the mdp file, but on > your system. Maybe you need to define a

Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

. How to make it work again and still keep the em.mdp the smallest, simplest possible? Thanks, Alan On 27 August 2014 at 17:09, Mark Abraham wrote: > You only need the integrator :-) Default for everything else works. > > Mark > On Aug 27, 2014 4:24 PM, "Alan" wrote: >

Re: [gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5)

Thanks Justin, I forgot to mention but my system is just on small molecule, without solvent, no box defined in principle. So, basically, I want to see if the topology is “OK” enough for GMX to not complain, like I used to do, before doing big things. Thanks, Alan On 27 October 2015 at 12:01

[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5)

element. Increase the box size or decrease rlist. And my md.mdp (which I didn’t test yet, and I fear it will likely fail too) is: integrator = md nsteps = 1000 If I could keep them working for both GMX 5 and 4.5 that would be great. Thanks, Alan -- Alan

Re: [gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

Nicolas, if you have created your files in Amber, then the conversion to GROMACS should be fine. You can find some details about it in https://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx Alan On 9 October 2015 at 12:39, Justin Lemkul wrote: > > > On 10/8/15 11:48 AM, Nicol

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

Hi Not because I developed ACPYPE, but if I’d like to be the most rigorous as possible, I’d go with ACPYPE and RED (http://q4md-forcefieldtools.org/). Alan On 29 May 2015 at 20:53, Ebert Maximilian wrote: > I continued to define good partial charges using the tools suggested. I > foun

Re: [gmx-users] gmx rmsdist: rmsmax vs. rmscmax

teractomic distances. I'm likely misunderstanding this tool... Thanks in advance for the help. Regards, Alan Manning On 03/16/15 04:24, Justin Lemkul wrote: On 3/15/15 6:36 PM, Alan Manning wrote: Hi What is the difference between the "rmsmax" and "rmscmax" v

[gmx-users] gmx rmsdist: rmsmax vs. rmscmax

Hi What is the difference between the "rmsmax" and "rmscmax" values written to the screen when running "gmx rmsdist"? Thanks. Regards, Alan Manning -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Writing out the neighbor list

ff; very doable for the single-domain case, but not already done for you. Mark On Mon, Mar 9, 2015 at 9:48 PM, Alan Manning wrote: Hi Is it possible to have Gromacs write out the neighbor lists as well as the trajectories? Thanks. Regards, Alan Manning -- Gromacs Users mailing list * Pl

[gmx-users] Writing out the neighbor list

Hi Is it possible to have Gromacs write out the neighbor lists as well as the trajectories? Thanks. Regards, Alan Manning -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Converting Amber parameters to gromacs parameters

In principle, if you have _prmtop_, _inpcrd_ files, then acpype -p _prmtop_ -x _inpcrd_ [-d] should be able to handle any situation, even Amber14. Alan On 16 December 2014 at 14:12, Magnus Lundborg wrote: > > Hi, > > Have a look at acpype. That should be able to convert fro

[gmx-users] updates about ACPYPE

/svnroot/ccpn/branches/stable/ccpn/python/acpype acpype or simply (for those who already have ACPYPE): svn update Many thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome

Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

Many thanks Mark! Alan On 27 August 2014 18:09, Mark Abraham wrote: > You only need the integrator :-) Default for everything else works. > > Mark > On Aug 27, 2014 4:24 PM, "Alan" wrote: > > > Hi there, > > > > I need a very simple em.mdp

[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

with GMX 5. Can someone suggest me the minimum alterations or completely new values so I could run a quick EM and MD? And if they were compatible to both GMX 4 and 5 that’d be great. Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics

Re: [gmx-users] Atomic charges: RESP or AM1-BCC

Dear Oliver, I’d recommend to try http://q4md-forcefieldtools.org/REDS/. If you did all right, it should t least confirm your RESP results. Alan On 19 May 2014 07:20, Oliver Schillinger wrote: > Hi everyone, > > I am trying to parametrize a ligand for use with the amber for

Re: [gmx-users] Simulating a 282 atom molecule. How do I split it into parts?

Well, allow me this suggestion. Consider using http://q4md-forcefieldtools.org/ to get the right charges, then update these charges in the mol2 file and run acpype with “-c user” option. For a quick test, you can use “-c gas”, which would give you charges via gasteiger method. Alan On 5 January

Re: [gmx-users] Acpype charge

I would suggest you to read the acpype paper http://www.biomedcentral.com/1756-0500/5/367 and the references within. Alan On 12 December 2013 19:37, kiana moghaddam wrote: > Dear GMX Users > > I 'm running MD Simulation between DNA-ligand interaction using parmbsc0 > force fi

Re: [gmx-users] Creating a topology file for small molecules

t? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics

Re: [gmx-users] ACPYPE FAILED: 'MolTopol' object has no attribute 'chiralGroups'

I haven’t upload the fix, but essentially, if you install openbabel, these error would disappear. Alan On 27 November 2013 18:48, Mahboobeh Eslami wrote: > hi my friends, please help me > > i use acpype for my ligand > > but i get following error: > > ACPYPE FAILED: &#x