Why not use the 'fixatomorder' command in cpptraj to fix your topology
and trajectory, then run MMPBSA.py using the reordered
topology/trajectory? E.g.,
parm myparm.parm7
trajin mytraj.nc
fixatomorder outprefix reordered
trajout reordered.nc
-Dan
On Mon, Oct 5, 2015 at 12:51 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Hello,
>
> I have an “artificial” molecule, which was obtained by removing portions of the original one in order to enhance the calculations in MMPBSA. In the complex and the receptor there is a disulfide bridge between CYX residues in different chains. All seems to be OK until I run the MMPBS.py where I get the error listed above.
> Atom 1512 is in the chain that contains the second CYX.
>
> I read the archive discussion http://archive.ambermd.org/201409/0451.html but there it does not offer a solution for running MMPBSA.py, rather it offers a solution in cpptraj.
> There is also a promise for a fix.
>
> Could you suggest what to do.
>
> Thanks for your help
> Roman Osman
> Department of Structural and Chemical Biology, Box 1677
> Mount Sinai School of Medicine
> New York, NY 10029
> roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 05 2015 - 12:30:04 PDT
