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

[Justin A. Lemkul]

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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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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