[gmx-users] pdb2gmx : treat CL as C

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 17 15:44:49 CET 2009


> What is the problem?  It looks like you got everything to work, but the .pdb
> file you've posted is misformatted on the CL lines:
> ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00
> C
> ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00
>  CL
> Note how the atom name "CL1" is shifted relative to "C14" so pdb2gmx handled
> it incorrectly.  Formatting is not merely a suggestion!

This is correct formatting, according to the PDB file format! Of the
four character positions denoting the atom name, the first two are
used to indicate the element.

But what is this talking about pdb2gmx if there's a hand written
.top/.itp file in stead of an .rtp entry? Of course it will fail. And
if that's not the problem, Nilesh is still not providing a proper
description of what he's doing.


Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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