[gmx-users] combine two pdb files

[masoud keramati]

yes it's true.
thank you all

On Sat, Nov 28, 2015 at 3:31 PM, Peter Stern <peter.stern at weizmann.ac.il>
wrote:

> 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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