[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

maria goranovic mariagoranovic at gmail.com
Fri Mar 25 11:09:57 CET 2011

Hello List

I want to change an ASP to a D-ASP. I think it should be possible by simply
changing 2 improper values around the chiral carbon to their opposite sign.
Instead of making a brand new residue, I thought I would take the topology
of an ASP generated by pdb2gmx, and simply change values manually in the
resulting .itp. However, this is not possible because gromacs wants to read
the dihedral parameters from the ffbonded.itp file. Is it possible for me to
explicitly state the parameters for these two dihedrals in my d-asp.itp
file? This will be the fastest solution to the problem because it precludes
making a new residue or defining new atoms types and so on. With the CHARMM
force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which we
are used to for gromos topologies.

The mailing list search function was down, so I could not explore prior
messages about this.



Maria G.
Technical University of Denmark
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