<br><br><div><span class="gmail_quote">On 7/20/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org" title="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org" title="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>From: priyanka srivastava <<a href="mailto:priyankaps4@yahoo.com" title="mailto:priyankaps4@yahoo.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
priyankaps4@yahoo.com</a>><br>Subject: [gmx-users] atom names do not match<br><br>Thanks again for your kind response.<br><br>I guess I will write down my problem once again :-)</blockquote><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Warning: atom names in 96_neatsys14.top and test.gro<br>don't match (NTM - C15)<br>Warning: atom names in 96_neatsys14.top and test.gro<br>don't match (CA - C12)<br>Warning: atom names in 96_neatsys14.top and test.gro<br>
don't match (CB - C11)<br>Warning: atom names in 96_neatsys14.top and test.gro<br>don't match (OA - PO4)<br>Warning: atom names in 96_neatsys14.top and test.gro<br>don't match (P - O13)<br><br>When I look at the atom types that are there in the
<br>.gro file they seem to be the problem, i.e. the<br>choline Nitrogen is represented as N only which refers<br>to a peptide N in gromacs. What should I do?<br>Please help me and also suggest me if I am going in<br>the right direction or not?
<br><br>eagerly waiting for the gromacs experts response,<br>warm regards,<br>Pri...<br><br></blockquote></div><br>
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. <br>
<br>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). <br>
<br>
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.<br>
<br>
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<br>
<br><br clear="all"><br>-- <br>greetings, Pim