[gmx-users] combine two pdb files

[Peter Stern]

Probably.  So follow Chandan Choudhury's suggestion to use editconf -resnr 1 to reorder the residue numbers too and then it should work.

Peter

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of masoud keramati
Sent: Saturday, November 28, 2015 1:12 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] combine two pdb files

hi

yes that's right. but it's renuber atoms not residues.
is the same residue number make an error?

tnx : )

On Sat, Nov 28, 2015 at 1:57 AM, Peter Stern <peter.stern at weizmann.ac.il>
wrote:

> AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file 
> since in any case it reorders them and renumbers them after adding 
> hydrogen atoms.  Did you try it?
>
> Regards,
> Peter
>
> Sent from my iPad
>
> > On 27 בנוב׳ 2015, at 22:28, masoud keramati 
> > <keramati.ma3oud at gmail.com>
> wrote:
> >
> > Hello
> >
> > I want to simulate two proteins and need to combine these two pdb 
> > files
> in
> > one.
> > important thing is the atom number. if combine with cat command it 
> > gives
> a
> > file that contain two atom with the same atom and residue number 
> > that
> will
> > make an error in simulation.
> > is there exist any way to combine these two pdb files to solve this
> problem?
> > I mean if first pdb finish with atom number n and residue number m 
> > then next pdb is start with atom number n+1 and residue number m+1.
> >
> > tnx
> > --
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