[gmx-users] special bond
Justin Lemkul
jalemkul at vt.edu
Tue Apr 29 14:28:45 CEST 2014
On 4/29/14, 5:18 AM, fantaman wrote:
> Dear Justin,
>
> thank you very much for your help!! Indeed it helped me fixing the problem!!
>
> Could I ask you also a brief question about special bonds? I have defined in
> specbond.dat a special bond between 2 atoms, say ATM1 & ATM2, of 2 different
> residues but belonging to the same chain, like this:
>
> 1
> RES1 ATM1 1 RES2 ATM2 1 0.288 RES1 RES2
>
> and afterwards I have defined in ffbonded.itp the bond gb_99 like this:
>
> #define gb_99 0.288 3.0402e+07
> ; ATM1 - ATM2 special bond
>
> and then at the end of the same file I have written down:
>
> ; bond-, angle- and dihedraltypes for specbonds:
> [ bondtypes ]
> ATM1 ATM2 2 gb_99
>
> By doing so, then pdb2gmx runs nicely but in the speptide.top file I do get
> in the [ bond ] section all the couples of ATM1 & ATM2 atoms, but no gb_99
> bond is there... Would you have any clue why? I have read that too strong a
> coupling constant might cause problems and I have therefore tried with a
> normal one, but still no gb_99 is there...
>
You need to differentiate between atom names and atom types. Names are used on
the molecule level, so that's what ATM1 and ATM2 are for. At the force field
level, you need to specify interactions in terms of atom types. Using ATM1 and
ATM2 has no effect in ffbonded.itp because there are no such atom types in the
force field.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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