[gmx-users] unknown cmap torsion between atoms
Mark.Abraham at anu.edu.au
Tue Nov 1 04:29:01 CET 2011
On 1/11/2011 2:16 PM, ram bio wrote:
> Hi Mark,
> Thanks for the response.
> 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.
I don't know. Either you, pdb2gmx or grompp has done something wrong.
> 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?
Lipids do not use CMAP.
> moreover, grompp also throws error as no default U-B types along with
> unknown CMAP torsion.
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.
> Could you please diagnose where the problem exists in my procedure and
> let me know.
No. I told you how to start to work out the problem and you seem to have
ignored it :-)
> On Mon, Oct 31, 2011 at 9:57 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 1/11/2011 1:24 PM, ram bio wrote:
> Dear Gromacs users,
> 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.
> Could someone please explain me what this error mean and how
> to overcome this.
> 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.
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