[gmx-users] Problem with phenylglycine MD
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 15 08:53:58 CET 2006
Ashutosh Jogalekar wrote:
> 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.
> Help will be really appreciated since I am stuck with this problem for
> Ashutosh Jogalekar
> Emory University, Atlanta, GA
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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