[gmx-users] a request regarding pdb2gmx and specbond.dat

francesco oteri francesco.oteri at gmail.com
Thu Mar 8 15:30:01 CET 2012

I agree it could be very useful. You can insert the bond hand-coding it in
the topology, but you need also to generate angle and dihedral.
This is very boring and error prone.


Il giorno 08 marzo 2012 12:32, Ehud Schreiber <schreib at compugen.co.il> ha

> Hi,****
> ** **
> The mechanism for specifying special bonds for the pdb2gmx program, using
> the specbond.dat file (manual section 5.6.7), seems to me not general
> enough. The characteristic length of the bond is specifiable, but the range
> of lengths for which a bond is assumed is hardcoded as +-10% of the
> characteristic length. I, for example, am perturbing structures using the
> Concoord method, and lengths of disulfide bonds sometimes vary by more than
> 10%.****
> I therefore suggest that two values would be added at the end of the line
> declaring a special bond, specifying the minimum and maximum lengths. These
> two values would be optional, so as not to break the existing arrangement,
> which would remain as the default. This should not require more than a few
> extra lines of code and would be, in my opinion, very useful.****
> ** **
> What do you say?****
> ** **
> Thanks,****
> Ehud Schreiber.****
> ** **
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Cordiali saluti, Dr.Oteri Francesco
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