Hi Mark,<br><br>Thanks for the response.<br>I have built this system (protein in popc bilayer using charmm GUI) and submitted the total built system to pdb2gmx, is this the reason for having unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot show any error. Cant the charmm gui built system be used in gromacs with charmm27ff.<br>
<br>Out of the 134 atoms for each popc in the structure file few initial atoms were not matching in the lipids.itp file under charmmff folder, so i changed the atom names in the lipid.itp under popc section to match with atom names in the structure file, is that could be reason?<br>
<br>moreover, grompp also throws error as no default U-B types along with unknown CMAP torsion.<br><br>Could you please diagnose where the problem exists in my procedure and let me know.<br><br>Thanks<br><br>Pramod<br><br>
<div class="gmail_quote">On Mon, Oct 31, 2011 at 9:57 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5">On 1/11/2011 1:24 PM, ram bio wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs users,<br>
<br>
I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381 8394 8397.<br>
<br>
Could someone please explain me what this error mean and how to overcome this.<br>
</blockquote>
<br></div></div>
It means you are somehow using CMAP on a dihedral whose atom types do not have a known CMAP function - "unknown CMAP torsion". You need to do some detective work on those atoms and their types to work out why.<br>
<br>
Mark<br><font color="#888888">
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