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

[Oliver Grant]

1. pdb2gmx, editconf and then solvate.
2. use trjconv and make a pdb.
3. Take 7 water molecules and put them in the top of your original pdb and
start again from there.



On 3 June 2010 09:34, NG HUI WEN <HuiWen.Ng at nottingham.edu.my> wrote:

>  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 <<
>
> Email has been scanned for viruses by UNMC email management service<http://www.nottingham.edu.my>
>
> >>
>  <<
>
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