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

[Nelson Cotrim]

Dear All,
Just to confirm what Justin said, my MD worked flawlessly with his
ffG43a1p files.
The only issue was that I had to change my pr.mdp and md.mdp files,
following a suggestion I found here: I changed the T coupling groups
to "Protein" and "Non-Protein" (I am using the same temperature for
the whole system anyway).
Many thanks for all your help.
Best regards,
Nelson


On Jan 18, 2008 5:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Dear All,
>
> In working with Nelson on his problem (below), I made some headway into figuring
> out what is going on with the ffG43a1p force field files.  I know a few others
> have asked questions about it across this list, so I thought I would send this
> out to everyone.
>
> By modifying a few entries in the .hdb file, the problems seem to be alleviated
> (as in, the residues are recognized and pdb2gmx proceeds without any errors).
> It seems that perhaps the formatting of the .hdb file has changed since a
> previous version of Gromacs, but this change has not been reflected in the
> ffG43a1p* files.  I made no changes to the parameters or the entries in the
> original files, only the formatting.
>
> If anyone has a need for the complete set of ffG43a1p files, please email me
> (off-list), and I will be happy to send them along.  If there is a widespread
> demand for them, I will upload them to the User Contributions site.  Hopefully
> they will work :)  I have not tested them extensively, but I looked into it
> because I was curious.
>
> -Justin
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
> > Nelson,
> >
> > 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.
> >
> > -Justin
> >
> > 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
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
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> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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