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 <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]>: > > > 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 <[EMAIL PROTECTED]>: > > > > > 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@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 [EMAIL PROTECTED] > > > 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 > > [EMAIL PROTECTED] | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > 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 > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Av. Bauhinia 400 CCS, Bl. E, sl 22 21941-590 Ilha do Fundão - Rio de Janeiro - RJ Brasil Tel: 55-21-2562-6759 Cel: 55-21-9267-3067 _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
