[gmx-users] Re: pdb2gmx eats a bond

[Thomas Schlesier]

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
>