[gmx-users] Chain merging problem (pdb2gmx)

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Apr 26 09:20:53 CEST 2006


On Tuesday 25 April 2006 22:28, Ashutosh Jogalekar wrote:
> Hello
> I have three peptide strands with the sequence HHQALVFFA. I am trying
> to create a .gro file of these. But I don' want to merge these chains
> together, as the N termini are not capped (NH3+)
> When I do pdb2gmx, even when I am not using the -merge option, the
> program is still merging the chains together. Since they are actually
> separate in reality, this is causing many problems, not the least of
> which is that the charge on the system is being cited as +1, when it
> should be +3.
> What should I do to get rid of this problem?

Correct your pdb file, so that each chain got a unique chain identifier, 
normally i do this with swiss pdb viewer ( http://www.expasy.org/spdbv/)

edit - rename current layer 

Our pdb should look like:

ATOM      1  N   SER A   1      45.156   8.138  75.085  0.00  0.00

The "A" after the residue name is the chain identifier.

> Thanks
> Ashutosh Jogalekar
> Emory University
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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