[gmx-users] CHarmm and popc membrane

[Chris Neale]

>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