[AMBER] Issues with running simulation after ParmEd conversion

From: Rohith Mohan <rmoha004.ucr.edu>
Date: Tue, 28 Jul 2015 16:30:26 -0700

Hello all,

I have a fairly large protein system (approximately 394651 atoms including
solvent) that I have minimized, heated and equilibrated in NAMD and am
trying to perform the production run in AMBER (with CUDA) so that I can use
a specific aMD method. I utilized the latest version of ParmEd to convert
the PDB (taken from the last frame of the NAMD equilibration trajectory)
and PSF using the CHARMM c36_aug14 topology and parameter files as shown in
the commands below:

chamber -param par_all36_prot.prm -param par_all36_lipid.prm -param
par_all36_cgenff.prm -str toppar_water_ions.str -psf
C3_full_solv_ionized.psf -crd C3_full_solv_ionized.pdb
outparm C3_equil.prmtop C3_equil.inpcrd

After several errors during production run attempts and troubleshooting, I
finally utilized cpptraj to check the structure and found that there were
many clashes with atoms in close contact (<.2 A) with each other. I also
verified that these clashes did not exist before conversion in the input
PDB. Additionally, I repeated the conversion process with a much smaller
system (~17,000 atoms) and found that there was no issues there so I think
the size of my system could be affecting the conversion.

I was wondering if anyone else had any issues with converting large systems
using ParmEd and might have any suggestions or guidance for me.

Rohith Mohan
UC Riverside
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jul 28 2015 - 17:00:03 PDT
Custom Search