[gmx-users] Re: good Atom type in gromacs with the AMBER ff port

Alan alanwilter at gmail.com
Thu Oct 1 09:51:07 CEST 2009

Hi there,

Please, let me suggest to look at acpypi.googlecode.com. You may find
at wikis some answers to your questions.

I hope it helps.


On Thu, Oct 1, 2009 at 02:34,  <gmx-users-request at gromacs.org> wrote:
> Message: 2
> Date: Thu, 01 Oct 2009 09:17:02 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] good Atom type in gromacs with the AMBER ff
>        port
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AC3E6EE.6060007 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> ABEL Stephane 175950 wrote:
>> Hi gromacs users
>> I have a newbie question about the atom type in gromacs. I would like to simulate a peptide with AMBER ff (ffamber03) in gromacs v.4.05 , so I have downloaded the ffamber files and followed the explanation given in Sorin's lab homepage. To neutralize my system i have added one CL- ion in the simulation box, but i am not sure it was good ion (in a other word the CL- ion compatible with the AMBER ff and not the default ion parameters). Here what i did
> Unfortunately at various points various strings have to match, and "CL-"
>  is different from "Cl-" from "CL"
>> - Added ions.itp file the following directive:
>> #ifdef _FF_AMBER99
>> [ moleculetype ]
>> ; molname       nrexcl
>> Cl-              1
> This one needs to match the contents of your [ system ] directive.
>> [ atoms ]
>> ; id    at type         res nr  residu name     at name  cg nr  charge   mass
>> 1     amber99_30        1       CL-             CL       1      -1       35.4530
> The one on the left needs to match the residue name field of your
> structure file, and the one on the right needs to match the name in the
> atom name field of your structure file. (If you're using pdb2gmx, that
> atom name field would need to match the name in the atom type database too!)
> I don't know which of these needs to match the name given on the genion
> command line, but it'll be one of them.
> Mark
>> #endif
>> - Use the following command with genion
>> genion_mpi -s ions.tpr -o beta-I-Ac-NH2_slv_AMBER_ions.gro -p topol.top -pname NA+ -nname CL- -nn 1 -> genion passes correctly
>> It is correct ? If not what is wrong ?
>> Thanks in advance for your help.
>> Stéphane

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)

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