[gmx-users] Regarding creating topology for molecule

Dilip H N cy16f01.dilip at nitk.edu.in
Mon Jul 10 12:06:30 CEST 2017

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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