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

[Justin A. Lemkul]

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
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> ========================================
>
> 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/
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



========================================

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/

========================================