Modeling of Gramicidin A

From: Jian Liu (bay__gulf618_at_sina.com)
Date: Mon Jun 29 2009 - 08:08:41 CDT

Hello all
D-amino acid residues and unusual end capping (the formyl groups at the N-termini, and the ethanolamide group at the C-terminus) make it is complicated to model Gramicidin A.

1. D-amino acid residues
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/  and
http://biophys.physics.missouri.edu/courses/phys4500-06/      
have give some instructions, but they all deal with it through
vmd> pdbalias residue DLE LEU
vmd> pdbalias residue DVA VAL
vmd> ...
vmd> guesscoord
Does it credibility when guessing the missing H atoms ?
or need we change some IC value in topology files as suggested in "topology file tutorial" ?

2. unusual end capping
The two caps is not containe in all kinds of topology of charmm FF neither.
http://biophys.physics.missouri.edu/courses/phys4500-06/ said that:"Topology entries were guessed for these residues; you'll find them at the very end of the topology file (common/top_all27_prot_lipid.inp)", but unfortunately i cannot find the file.

"topology file tutorial" also gives a method to deal with this problem by borrowing the FF parameters from a similar group.
Does this is the only way ?

best wishes
Jian Liu

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