[gmx-users] modified residues and residual charge

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Tue Feb 24 15:00:06 CET 2015


Dear All,

   I was wondering how people deal with the issue of generating special amino acids in Gaussian, then being left with residual charge upon removing blocking blocks.  The process I follow is:

1.  Build the modified amino acid (side chain is non-standard) in Gaussian, with blocking groups on the main chain N and carbonyl carbon (acetyl, and -NHCH3, respectively) and run Gaussian.

2.  Take resulting structure and feed into antechamber from AmberTools.  One can use the charges from Gaussian, or allow antechamber to assign RESP or other charges (haven't tried the others).

3.  Edit resulting mol2 file, remove the blocking groups and use parmchk and tleap to output Amber force field files.

4.  Use acpype to convert to gromacs type files.

5.  Modify a copy of the force field files to include this new amino acid type.

The problem arises when removing the blocking groups, since one is left with residual fractional charge for the residue (about -0.1 in this case).  I could simply divide up this charge among all the main chain atoms (add 0.025 to each), but perhaps there is a better way.




Harry M. Greenblatt

Associate Staff Scientist

Dept of Structural Biology

Weizmann Institute of Science        Phone:  972-8-934-3625

234 Herzl St.                        Facsimile:   972-8-934-4159

Rehovot, 76100


Harry.Greenblatt at weizmann.ac.il<mailto:Harry.Greenblatt at weizmann.ac.il>

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