[gmx-users] Problems with non standar residue combining Amber and GAFF

Justin Lemkul jalemkul at vt.edu
Tue Nov 22 21:14:25 CET 2016

On 11/21/16 6:03 AM, Rebeca García Fandiño wrote:
> 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.

Yes, you're attempting to #include a file that isn't even in GROMACS format, so 
naturally grompp is going to fail.

> How could I properly translate the information contained in gaff.dat to the files ffbonded.itp in Amber?

You'll have to consult the AMBER documentation for the format and units of its 
contents, then translate to the appropriate units and format for GROMACS.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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