Peggy Yao wrote:
Dear all,
I am new to MD simulation. I am trying to do an all-atom MD simulation
with explicit water of a protein which has a few missing side-chain
atoms of a GLN residue.
1. Which force field would you recommend? The protein is an x-ray
crystal structure, about 200 residues. Hydrogen atoms and hydrogen
bonding are important.
2. According to the Gromacs manual, OPLS is recommended for all-atom MD
simulation. However, when I tried to use OPLS-AA as the force field,
pdb2gmx returned me an error:
Fatal error:
Atom CG not found in residue GLN82 while adding hydrogens
Right, because as you said before, you have missing atoms! This is not a
problem that can be magically fixed by Gromacs tools or specific force fields.
Then I tried all other force fields. Only the following didn't give that
error:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: [DEPRECATED] Gromacs force field (see manual)
Is any of them good enough? If not, is there any way (such as a good
free software) to fill in the missing atoms?
That depends on your definition of "good enough." The big DEPRECATED warning on
ffgmx suggests (very strongly) that it should not be used. The decision among
Gromos96 variants is yours, based on reading the primary literature for the
parameter sets (conveniently cited in the pdb2gmx output!)
As for free software, AmberTools is now available so that you can use xLeap to
modify structures. Other possibilities might include DeepView (Swiss-PDBViewer)
or Modeller.
-Justin
Thanks a lot!
Peggy
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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