On 7/20/06,
[EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:
From: priyanka srivastava < [EMAIL PROTECTED]>
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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