[gmx-users] How to remove H atom from residue in gro file?

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 17 22:53:13 CET 2008


A long while back, a member of our lab contemplated simulating a phosphorylated
protein, but ran into some issues as well.  I tried to help him by editing the
ffG43a1p files, and I seem to remember making some headway.  If you'd like, you
can send me your .pdb file (off-list) and I'll test it against my ffG43a1p
files.  If it works, I can send you my modifications.  I made no changes to the
force field parameters, only the formatting of the files themselves.


Quoting Nelson Cotrim <nhcotrim at gmail.com>:

> Hi Justin,
> Thanks for the reply.
> Yes, I used PRODRG Beta. Thanks for the heads up about the charges.
> The error I got using ffG43a1 was this:
> >Fatal error:
> > wrong format in input file ffG43a1p.hdb on line
> >        2       7       OW
> which was also described here:
> http://www.gromacs.org/pipermail/gmx-users/2007-August/028977.html
> but that did not solve my problem. I removed all the unnecessary
> entries from the hdb file, keeping only the SEP and P data, and then
> there was another error in yet another ffG43a1p file (I don't remember
> which one right now). I removed all ffG43a1p files and rolled back the
> files changed by ffG43a1p to the original ones from Gromacs 3.3.1 and
> tried PRODRG.
> So far, everything is going smoothly -  I am running the dynamic even
> so (it's a small one, takes me just two days of computer time and
> there are no other MDs to run), to make sure everything goes right -
> the PO3 keeps its tetrahedrical shape, grompp and mdrun runs
> smoothly... I just will not be able to use the results because there
> is this extra hydrogen atom which I do not know how to remove from the
> .gro and .top files.
> Nelson
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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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