Hello
I am trying to run an MD on a short tripeptide contaning phenyglycine
(PHG)- that is with the phenyl ring direct attached to the alpha
carbon. I am using the OPLS force field. The peptide is (PHE-PHG-LEU)
I modified the .rtp and .hdb files accordingly. I put in the atoms,
bonds, and improper dihedrals in the .rtp file. I put in the new name
PHG in the aminoacids.dat file.
Everything seems to start ok, until I am done with the energy
minimization. There is no error, and the minimization ends smoothly.
However, at the end, the alpha carbon is distorted; it's not
tetrahedral and the hydrogen bends towards the phenyl ring. Not
suprisingly, in the rest of the simulation, the distortion is not
relieved. I don't know what's going wrong, since there is no error as
such and the .rtp and the .hdb files have been modified in an apt
manner.
One thing is that there are no parameters for some of the dihedrals
in the OPLS force field. So when I am doing grompp for the EM, the
program naturally puts zeros in front of those dihedrals. Two
examples are:
N CA CG CD1
HA CA CG CD1
Could this be causing the carbon to distort? If so, where can I get
the parameters for these dihedrals?
Help will be really appreciated since I am stuck with this problem
for days!
Thanks
Ashutosh Jogalekar
Emory University, Atlanta, GA
USA
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