[gmx-users] Regarding creating topology for molecule

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 10 14:01:48 CEST 2017


The rdf should be constructed from specially constructed index groups, eg
from all N in a specified molecule. Don't try to involve pdb2gmx, it needs
to match the names to the rtp files.


On Mon, 10 Jul 2017 12:06 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> 1] I want to simulate A and B mixtures...but the problem is tht in both the
> say atoms of nitrogen's of both A and B molecules are labelled as N
> only....which during the indexing for RDF creates problems...
> So in the CHARMM FF .rtp file, i changed the nitrogen (of B molecule) N
> into N1 and thn saved it, and thn did the changes in atom type from N to N1
> in  .pdb/gro file (of B molecule), since now both the nitrogen is labelled
> different in B molecule, and hence now the nitrogen's are labelled
> differently in A and B molecules.
> thn i ran the command as :-
>       gmx pdb2gmx -f a.pdb -o a.gro
> but still i am getting the error as:-
> Atom N1 in residue XXX 2 was not found in rtp entry XXX with x atoms
> while sorting atoms.
> Why is this error coming inspite of changing the atom type from N to N1
> (ie.,redefined the atoms and checked there is no mismatch between them) in
> the .rtp file, Or still should i do any changes in any other files..??
>  but still i am getting this error... how to solve this error..??
> 2] In general, if the atoms are labelled in same type/name for different
> molecules in the .rtp files/any other files, thn how can i correct it and
> get a correct topology file, and get the index's correctly of the atoms
> named same in different molecules, without getting overlapped..??
> Thank you...
> --
> With Best Regards,
> Ph.D Student
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