Dear Amber Users and Developers,
I am working on
HCA II taking 2cba.pdb. It does not have two N-terminal residues. So,
to get proper residue number I attach two N-terminal residues by
SWISS-PDB VIEWER. Unfortunately there have been some unusual bonds
between residue 1 and some crystal waters(resid 270,279,295). I
thought after minimization structure would be good. When I run
pmemd.cuda to minimize there is no change in that portion. VDW
energies are too large that they are not coming. But if I run sander
the unusual bonds are broken and VDW energy values are coming from the
NSTEP = 50. (ntpr = 50). So, starting with sander can I continue my
rest of simulation with pmemd.cuda?
Sanjib Paul
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 23 2013 - 22:30:02 PST
