[gmx-users] couldn't find topology match for atom type opls_102

while running grommp_d I see this error. Couldn't find topology match for atomtype opls_102 Aborted my .pdb and .top and .gro file attached.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Charge groups in Charmm for lipids

The new GROMACS 4.5.4 version of the CHARMM36 force field files are now uploaded on the GROMACS website contributions section. Just to note that if anyone downloaded the 4.5.4 version uploaded a few hours ago then the atomtypes.atp file was incomplete and should download this new version.

Re: [gmx-users] couldn't find topology match for atom type opls_102

Amir Abbasi wrote: while running grommp_d I see this error. Couldn't find topology match for atomtype opls_102 Aborted The error arises when you try to use an atom type in an implicit solvent calculation which does not have proper GB parameters. opls_102 corresponds to the OPLS-UA N

Re: [gmx-users] couldn't find topology match for atom type opls_102

Amir Abbasi wrote: Thanks,how can I solve it? I already provided on suggestion, and without a clear description of what you're doing and what you've tried, I won't venture any further guesswork. -Justin *From:*

[gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute

I encountered the exact same error with Gromacs-4.5 as posted by Sunita Patel back in October 2010 and could not find any solution in the gmx_thread. The error was: Failed to execute command: /home/path-to-dssp -na dd3sOJn3 ddZl9dcf /dev/null 2 /dev/null I found that the do_dssp fails to fork

[gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitive for me since the

[gmx-users] Gromacs 4.0.7 on Blue Gene/P

Dear all, I have installed the gromacs 4.0.7 on the Blue Gene/P according to the instructions on the gromacs webpage, but after submitting my testing system of water box around 10 nm, I found the simulation went really slow, or not running at all, output files are always 0 bytes. the md.log file

Re: [gmx-users] charge assignment for the anomeric carbon in 53a6 ff

Yun Shi wrote: Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field. I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of