Re: [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-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of masoud 
keramati
Sent: Saturday, November 28, 2015 1:12 PM
To: gmx-us...@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.st...@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.ma3...@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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
> > or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [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.st...@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-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of masoud
> keramati
> Sent: Saturday, November 28, 2015 1:12 PM
> To: gmx-us...@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.st...@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.ma3...@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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > send a mail to gmx-users-requ...@gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] combine two pdb files

[masoud keramati]

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 
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 
> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] combine two pdb files

[Chandan Choudhury]

You can try using editconf with resnr 1.
On Nov 28, 2015 3:57 AM, "Peter Stern"  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 
> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] combine two pdb files

[Peter Stern]

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  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
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
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> mail to gmx-users-requ...@gromacs.org.
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