You are right, overlooked the line.
And thanks for the idea with the short run, i'm happy with anything, so
that i don't must look into more then 300 bonds.
Greetings
Thomas
Thomas Schlesier wrote:
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 -ter option is listed for me in 4.0.7:
/usr/local/gmx_407/bin/pdb2gmx -h
...
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
...
The option certainly works, if that's the concern.
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?
I don't know all of the underlying code, but I frequently see a bond removed
from most of my protein structures.
Has anybody an idea which could be the fastest way to find out which
bond is missing?
Run a short MD and see if any of your atoms drift away :)
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)?
Potentially, but until you test to see if any bonds are actually missing,
there's nothing to diagnose in these sections.
-Justin
Greetings
Thomas
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