[gmx-users] problems with chain IDs for huge complex

[Tsjerk Wassenaar]

Hi Tomek,

Process each chain separately with pdb2gmx, rename the moleculetypes and
combine them again. This is scriptable, but not entirely trivial. Renaming
the moleculetype takes something like

sed '/\[ *moleculetype *\]/{p;n;s/^.*$/NEWMOLECULETYPE/p}' itpfile

Hope it helps,

Tsjerk




On Mon, Nov 18, 2013 at 8:25 PM, Tomek Wlodarski
<tomek.wlodarski at gmail.com>wrote:

> As far as I remember in pdb format you can only use one character for chain
> id.
>
>
>
> On Mon, Nov 18, 2013 at 7:05 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
> > How about naming your chains AA-AZ then BA-BZ? You probably need to
> change
> > the chain names in the original structures rather than just renaming the
> > files.
> >
> > > Hi,
> > >
> > > I am preparing simulation of the ribosome and because of it size I am
> > > force
> > > to use A-Z and a-z to name all chains...
> > > With pdb2gmx it is not a problem but with grompp I am ending up with
> this
> > > error (gromacs 4.6.3):
> > >
> > > Fatal error:
> > > moleculetype Protein_chain_b is redefined
> > >
> > > I figured out that for grompp Protein_chain_b and Protein_chain_B are
> the
> > > same entry - and hence error...
> > > I changed the name of files in this fashion:
> > > Protein_chain_b -> Protein_chain_bb etc
> > > And now grompp was able to read them but it found out that there is
> > > different number of atoms between top and gro file..
> > > Any ideas or suggestions?
> > > Thanks.
> > > Best
> > >
> > > tomek
> > > --
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-- 
Tsjerk A. Wassenaar, Ph.D.