[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 27 19:39:39 CEST 2008

Ragnarok sdf wrote:
> Hello Justin. You asked about adding solvents or ions. Well I added 
> solvent to the box using genbox, but the non integer total charge comes 
> from the beggining of the proccess, directly from pdb2gmx. Ions didn't 
> have the chance to get to that part, since my grompp command gives out 
> error about bond parameters, angles and stuff.

That's what I was asking - grompp is what's giving you the error, so what have 
you done since pdb2gmx?

> I've tried to use the structure directly from my pdb file, but that 
> didn't work as well. Then I tried using the NAB server to create a 
> double helix. And that does not seem to work as well.
> You told me to take a look at the last line of my itp files generated 
> from pdb2gmx and look for qtot. The problem is that there is no qtot 
> whatsoever on my itp files bonds section.

Apologies for my earlier typo.  What you want is the last line *before* the 
bonds section (i.e., the last atom entry).  There should be a commented-out 
section, i.e. ;qtot -11

> Maybe I could use some other software to create my double helix...I mean 
> wouldn't it be easier just to start over with a system you know it 
> works? If you have any suggestions on that, I do appreciate.

It looks like you're working with PDB entry 1VKX, based on the naming of your 
files.  Is that correct?  If so, I can try to process the same .pdb file and see 
if I'm getting the same issues.


> Thank you again
> Fabrício Bracht
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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