On Sun, Aug 18, 2013 at 7:17 PM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Dear AMBER list,
>
> How do I get this error at unrestrained NPT equilibration since I can load
> and visualize in VMD the prmtop and .rst file from NVT equilibration?
> The number of atoms in the .rst file is the same as in the .prmtop. Below
> is the configuration file I used in NVT.
>
This is a bug in tleap that results when you combine two separate molecules
using the 'bond' command in tleap. It is a bug in tleap that is known, but
has not yet been fixed.
There is a relatively simple workaround in either cpptraj or ParmEd (make
sure you have AmberTools 13 fully up-to-date).
Using ParmEd, try this:
parmed.py -p <your_prmtop> << EOF
loadRestrt <your_restart>
setMolecules solute_ions True
parmout <reordered_prmtop> <reordered_restrt>
EOF
reordered_prmtop and reordered_restrt should then work.
The error, in case you are curious, is that the SOLVENT_POINTERS and
ATOMS_PER_MOLECULE sections of the prmtop are structured under the
assumption that all of the molecules are composed of consecutive atoms.
However, if molecules 1 and 3 are combined via a 'bond' command in tleap,
then the atoms are not properly reordered to satisfy this assumption. This
results in a broken ATOMS_PER_MOLECULE section of the prmtop which can
later result in very strange errors (e.g., segfaults) in sander and pmemd.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 18 2013 - 18:30:03 PDT
