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

Ehud Schreiber schreib at compugen.co.il
Thu Mar 8 12:32:17 CET 2012



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?



Ehud Schreiber.


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