[gmx-users] Re: pdb2gmx - sorted!

dr.horsfield at physics.org dr.horsfield at physics.org
Tue Sep 3 09:26:17 CEST 2002


Last week I posted a message about a "problem" with pdb2gmx (see below).  
Once again it was mostly user error. (I am providing this message for the
benefit of the archives). For some reason a strand label had been
introduced for part of the strand, but not for the rest. pdb2gmx was just
doing its job!

The termination bug I still cannot explain.



On Fri, 30 Aug 2002 dr.horsfield at physics.org wrote:

> Hi,
> Is it possible to pursuade pdb2gmx not to break my nice single stranded
> protein into three strands?
> Using -merge does not work because there is a second problem. pdb2gmx
> tries to put a break before a PRO residue, and then it has trouble with
> the N termination. I get the message:
>   Fatal error: atom H not found in residue 557PRO while combining tdb and rtp
> Without the -merge option there is no error message.
> Cheers,
> Andrew

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