[gmx-users] missing parameters in auto-generated topology file?
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 6 20:50:18 CEST 2011
Yun Shi wrote:
> Hi all,
> I used pdb2gmx and selected amber99sb for generation of itp files of a
> normal peptide within GROMACS 4.5.4.
> But I saw that all the bonds, angles, and dihedral parameters (c0, c1,
> c2 ...) were not present in the itp file, while only funct is defined.
> It seems the same thing happens with opls ff.
> So I wonder if those parameters are automatically generated according to
> corresponding atom types when implementing grompp? What would happen if
Yes, they're read from ffnonbonded.itp.
> I have exotic species and some atomic sequences are not defined in the
> [ angletypes ] or [ dihedraltypes ] section of amber99sb.ff/ffboned.itp ?
You'd get a fatal error that there are no default bonded types for those
> In the other case, when I used amb2gmx.pl <http://amb2gmx.pl> to convert
> glycam force field-parametized prmtop file to gromacs top file, I saw
> something like:
> [ dihedrals ]
> ;i j k l func C0 ... C5
> 19 18 20 21 3 0.75312 2.25936 0.00000
> -3.01248 0.00000 0.00000 ;
> 41 1 18 19 3 0.20920 0.62760 0.00000
> -0.83680 0.00000 0.00000 ;
> Although I understand '3' in the fifth column indicates a
> Ryckaert-Bellemans-potential function, but what parameters are those
> numbers followed (0.75312 2.25936 0.00000 -3.01248
> 0.00000 0.00000) correspond to?
Please see manual section 4.2.12 and the table therein pertaining to
Ryckaert-Bellemans dihedral coefficients.
> Thanks for any help!
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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