Ashutosh Jogalekar wrote:
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?
Yes, the dihedrals and angles are the only forces involved in keeping
the conformation tetrahedral. Are you sure you have described the
Ha-Ca-Cg angle correctly?
For the dihedrals you may want to look at a similar dihedral, e.g.
Ca-Cb-Cg-Cd1
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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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