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

[Mark Abraham]

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
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