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On 1/11/2011 2:16 PM, ram bio wrote:
<blockquote
cite="mid:CA+iwn+YfkM3sD0qTGW2En0df8CgtoX-UURT6N8dygK9Nw4gF3w@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
I don't know. Either you, pdb2gmx or grompp has done something
wrong.<br>
<br>
<blockquote
cite="mid:CA+iwn+YfkM3sD0qTGW2En0df8CgtoX-UURT6N8dygK9Nw4gF3w@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Lipids do not use CMAP.<br>
<br>
<blockquote
cite="mid:CA+iwn+YfkM3sD0qTGW2En0df8CgtoX-UURT6N8dygK9Nw4gF3w@mail.gmail.com"
type="cite">
<br>
moreover, grompp also throws error as no default U-B types along
with unknown CMAP torsion.<br>
</blockquote>
<br>
So you have some atom types for which the angle potentials are
defined when the CMAP is not. That doesn't help find what atom types
you are using that do not have CMAP definitions.<br>
<br>
<blockquote
cite="mid:CA+iwn+YfkM3sD0qTGW2En0df8CgtoX-UURT6N8dygK9Nw4gF3w@mail.gmail.com"
type="cite"><br>
Could you please diagnose where the problem exists in my procedure
and let me know.<br>
</blockquote>
<br>
No. I told you how to start to work out the problem and you seem to
have ignored it :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+iwn+YfkM3sD0qTGW2En0df8CgtoX-UURT6N8dygK9Nw4gF3w@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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 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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