[gmx-users] charge groups

[Justin A. Lemkul]

Liu Shiyong wrote:

> Fatal error:
> atoms 4176 and 4182 in charge group 1767 are in different energy groups
> 
> PDB:
> ATOM   4176  OG  SER A 541     -13.599  44.346  39.228  1.00  0.00      
> S    1
> ATOM   4177  N   ALA A 542     -12.827  48.211  42.079  1.00  0.00      
> A    1
> ATOM   4178  CA  ALA A 542     -12.788  48.960  43.342  1.00  0.00      
> A    1
> ATOM   4179  C   ALA A 542     -12.052  50.279  43.097  1.00  0.00      
> A    1
> ATOM   4180  O   ALA A 542     -12.096  50.830  41.993  1.00  0.00      
> A    1
> ATOM   4181  CB  ALA A 542     -12.084  48.160  44.447  1.00  0.00      
> A    1
> ATOM      1  N   THR B   1      22.984  77.078   8.100  1.00 20.55      
> T    N

Using a structure file to understand a topology problem will give you nothing 
useful.  Charge groups are spelled out in the .top, so look there.  I suspect 
you are once again using the wrong structure file for whatever you're doing. 
This .pdb file does not have any hydrogens, which means that this structure was 
not processed by pdb2gmx under any force field (even a UA one), and thus will 
not correspond to your topology whatsoever.

-Justin

> 
> 
> 
> -- 
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu 
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab:    http://vakser.bioinformatics.ku.edu/people
> Phone:      (785) 864-1962
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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