[gmx-users] Re: pdb2gmx eats a bond
schlesi at uni-mainz.de
Wed Sep 22 20:11:06 CEST 2010
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.
> 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.
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