Hi Chris,
>
> I believe that the latest response had the wrong subject, so I am
> changing it back.
>
> Pär, two comments:
> First, does that option really exist?
>
> $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z
> 2>&1; cat z|grep nochargegrp|wc -l
>
The name flag is listed as [no]chargegrp
>
> Second, I am not entirely convinced that one can discount the need for
> gromacs-style charge groups. When CHARMM includes an atom in the
> cutoff, it includes the entire charge group, but that doesn't mean the
> algorithms of CHARMM and gromacs are entirely the same
That's why I said if you know what you're doing :)
>
> I gather that the large charge group listed below is the one that is
> spurring the message:
>
> GROUP ! H31
> ATOM N NTL -0.60 ! |
> ATOM C11 CTL2 -0.10 ! H33-C13-H32
> ATOM C12 CTL5 -0.35 ! |
> ATOM C13 CTL5 -0.35 ! H21 | H43
> ATOM C14 CTL5 -0.35 ! | | |
> ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+)
> ATOM H12 HL 0.25 ! | | |
> ATOM H21 HL 0.25 ! H23 | H41
> ATOM H22 HL 0.25 ! |
> ATOM H23 HL 0.25 ! |
> ATOM H31 HL 0.25 ! |
> ATOM H32 HL 0.25 ! H11-C11-H12
> ATOM H33 HL 0.25 ! |
> ATOM H41 HL 0.25 ! |
> ATOM H42 HL 0.25 ! |
> ATOM H43 HL 0.25 ! |
Yes, and probably one charge group in the arginine residue(s).
/Pär
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