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

Ragnarok sdf fabracht1 at gmail.com
Wed Aug 27 18:30:09 CEST 2008

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.
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.
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.
Thank you again
Fabrício Bracht
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