[gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")

[Pär Bjelkmar]

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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