[gmx-users] special bond

[Justin Lemkul]

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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