[gmx-users] pdb2gmx renumbers the residues in my pdb file

[NG HUI WEN]

Looks like I've got some work to do. Thanks Mark!

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Thursday, June 03, 2010 4:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file

 



----- Original Message -----
From: NG HUI WEN <HuiWen.Ng at nottingham.edu.my>
Date: Thursday, June 3, 2010 18:08
Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file
To: gmx-users at gromacs.org

> Hi,

>  

> I'm a new gromacs user. I have encountered a problem with pdb2gmx
where it automatically renumbers the residues in my pdb file. 

>  

> For instance, the first residue in my protein F8 has become F1 - this
affects all the residues in the protein, something I find rather
inconvenient.

>  

> I've been searching the archive for previous posts which might have a
solution to this but no luck so far. I might have been wrong. Many
thanks for your help.


I think you're out of luck. IIRC the facility you want is implemented in
the development version, but not yet released. If you re-renumber by
hand, then I suspect everything will be fine after that. grompp just
needs something whose atom and residue naming and ordering matches the
.top... how you produce that doesn't matter to it.

Mark << 

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<http://www.nottingham.edu.my> 

>> 

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