That's why I said if you know what you're doing :)
ok, fair enough.
The name flag is listed as [no]chargegrp
I still don't see it (see below), is this [no]chargegrp new in the cvs ?
I'm pretty sure that you're not referring to [no]lys, etc.
$ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z
2>&1; cat z|grep charge
encads Encad all-atom force field, using scaled-down vacuum charges
encadv Encad all-atom force field, using full solvent charges
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
-[no]arg bool no Interactive Arganine selection, iso charged
-[no]asp bool no Interactive Aspartic Acid selection, iso charged
-[no]glu bool no Interactive Glutamic Acid selection, iso charged
##
Chris.
-- original message --
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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