[gmx-users] Re: gmx-users Digest, Vol 27, Issue 64

pim schravendijk pimlists at googlemail.com
Thu Jul 20 18:27:52 CEST 2006


On 7/20/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org >
wrote:
>
>
> From: priyanka srivastava < priyankaps4 at yahoo.com>
> Subject: [gmx-users] atom names do not match
>
> Thanks again for your kind response.
>
> I guess I will write down my problem once again :-)


Warning: atom names in 96_neatsys14.top and test.gro
> don't match (NTM - C15)
> Warning: atom names in 96_neatsys14.top and test.gro
> don't match (CA - C12)
> Warning: atom names in 96_neatsys14.top and test.gro
> don't match (CB - C11)
> Warning: atom names in 96_neatsys14.top and test.gro
> don't match (OA - PO4)
> Warning: atom names in 96_neatsys14.top and test.gro
> don't match (P - O13)
>
> When I look at the atom types that are there in the
> .gro file they seem to be the problem, i.e. the
> choline Nitrogen is represented as N only which refers
> to a peptide N in gromacs. What should I do?
> Please help me and also suggest me if I am going in
> the right direction or not?
>
> eagerly waiting for the gromacs experts response,
> warm regards,
> Pri...
>
>
The names don't have to be the same, but in your case, it really looks like
there is mistake in the order: e.g. is this a P or an O ? (P - O13) etc.

What you really have to take care of is that the sequence of molecules in
your gro file is the same as the sequence you mention in the [ molecules]
section of topol.top. First, check that (it's a straightforward mistake and
easy to solve).

Otherwise, the sequence of atoms in the chains in the gro files might be
different from the topology. Then you'd have to change either the .gro or
the .top to make sure they are the same.

If all that is ok, then, if you include the .itp files and, the atom
parameters should be ok when you mention the moleculenames as mentioned in
the .itp file in the [molecules] part of the topol.top file



-- 
greetings, Pim
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