[gmx-users] Problems with non standar residue combining Amber and GAFF
Rebeca García Fandiño
regafan at hotmail.com
Mon Nov 21 12:03:50 CET 2016
Dear Gromacs users,
I am trying to add a new residue into a peptide composed of standar residues. For that I have used Antechamber to get a starting topology for that residue, obtained the corresponding .itp file in GROMACS (using amb2gmx.pl) and then modified the corresponding files in Amber99sb.ff force field (aminoacids.rtp, aminoacids.arn, atomtypes.dat, etc) incorporating the information of this new residue.
In a first approximation I have tried to include directly the file gaff.dat into forcefield.itp (#include "gaff.dat"), but then I also separated the different sections of gaff.dat and tried to included into ffbonded.itp file separately. In both cases pdb2gmx works without errors. However, when I execute grompp, I get errors complaing about gaff parameters (for example " Too few gb parameters for type br-br").
I have noticed that the type of data of gaff.dat file is not the same than the both files is not the same than that found in ffbonded.itp. For example, in ffbonded.itp from Amber:
[ bondtypes ]
; i j func b0 kb
C C 1 0.1525 259408.0 ; new99
C OS 1 0.1323 376560.0 ; new99
C H4 1 0.1080 307105.6 ; new99
whereas the analogous section in gaff.dat is:
ow-hw 553.0 0.9572 TIP3P water
br-br 123.2 2.542 SOURCE1 4 0.0000 0.0000
br-c 240.3 1.946 SOURCE2 2 0.0285 0.0285
br-c1 352.7 1.787 SOURCE2 4 0.0022 0.0024
So, I suppose my errors come from the non correct definition of bondtypes, etc of the gaff parameters from my new residue.
How could I properly translate the information contained in gaff.dat to the files ffbonded.itp in Amber?
Thanks a lot for your help.
Dr. Rebeca Garcia
Santiago de Compostela University
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