Hello. I have been trying to figure out why my simulations of a zinc
protein with a water molecule bound to the zinc atom were failing
without any warning. I think I found out what the problem is. While
inspecting the the catalytic site (the residues from the active site
were parameterized using the MTK++ procedure. To see more details on
this, see
http://archive.ambermd.org/201208/0174.html ), I discovered
that the angle between the H1-O-H2 atoms of the water molecule was
practically zero. I mean, they really collapsed onto each other. I
think the only thing that was holding them from actually collapsing
was the small vanderwalls parameters I introduced in order to solve
another problem regarding the charge distribution...etc (not really
the discussion here). The problem is that the parameters for this
particular angle is described in the .frcmod file. The line :
HW-OW-HW 103.000 104.520
should have worked, right?
When I check the parameters of the prmtop file using parmed.py, I find
that there are no angle parameters for these 3 atoms. None whatsoever.
I tried introducing them with parmed.py by using the command
setAngles, but when I try to save the modified prmtop file I get:
Outputting Amber topology file 1g5c_pre1.prmtop
MoleculeError: Molecule atoms are not contiguous!
Does parmed.py have problems with solvated systems?
Then I tried introducing restraints while doing the tleap routine, but
since I am using pmemd.cuda, pmemd kindly told me that restraints are
no longer supported by pmemd:
ERROR: PMEMD no longer allows constraints in prmtop!
| The prmtop must have mbona=nbona, mtheta=ntheta, mphia=nphia.
How can I solve this?
Thank you
Fabrício
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Received on Fri Sep 14 2012 - 13:00:02 PDT
