[gmx-users] pdb2gmx eats a bond
schlesi at uni-mainz.de
Wed Sep 22 17:26:59 CEST 2010
i have built an .rtp entry for a molecule with 310 bonds, for the opls
force field. For pdb2gmx i use the following command (version 4.0.7)
*pdb2gmx -f CAT.pdb -o -p -ignh -ter*
-ter is there because it is no protein, and use no C- and N-terminus
(since there are none).
Her one question, the option -ter works (i think) but it is not listed with
Are there any reasons.
The relevant output line of pdb2gmx is then
*Number of bonds was 310, now 309*
-> So pdb2gmx ate a bond.
Has anybody an idea why this happens?
Has anybody an idea which could be the fastest way to find out which
bond is missing?
Are the [ angles ] and [ dihedrals ] section also affected by this
(since if i understood it correctly pdb2gmx uses the [ bonds ] section
to determine the other two sections)?
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