[gmx-users] pdb2gmx eats a bond

Thomas Schlesier schlesi at uni-mainz.de
Wed Sep 22 17:26:59 CEST 2010

Hi all,
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
pdb2gmx -h
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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