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

[Stephane Abel]

Ok ! Thank you everybody for your help

Stephane
>
> Message: 3
> Date: Wed, 30 Sep 2009 19:36:26 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> 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: <4AC3EB7A.6020507 at vt.edu>
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>
>
> 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
>>
>> - Added ions.itp file the following directive:
>>
>> #ifdef _FF_AMBER99 [ moleculetype ] ; molname       nrexcl Cl-              1
>>
>>
>> [ atoms ] ; id    at type         res nr  residu name     at name  cg nr
>> charge   mass 1     amber99_30        1       CL-             CL       1
>> -1       35.4530 #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 ?
>>
>>     
>
> Why wouldn't it be?  There's only one entry for Cl- in ffamber03.atp.  Makes the 
> choice fairly easy :)
>
> -Justin
>
>   
>> Thanks in advance for your help.
>>
>> Stéphane _______________________________________________ gmx-users mailing
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>>     
>
>