Hi :) Maybe these little scripts are useful...
The first, titratable.sh (use: titratable.sh file.pdb), generates a list of residues for which the protonation state can be set, including the termini. The second, gmxquery.sh (use: titratable.sh file.pdb | gmxquery.sh) gives a series of 0 1 2, according to the protonation states desired. So, titratable.sh file.pdb | gmxquery.sh | pdb2gmx -f file.pdb -inter should be close to what you want. The output from titratable.sh can also be modified prior to piping it through gmxquery. And that can be easily scripted :) Do note that it doesn't deal with SS bonds. Hope it helps, Tsjerk On Tue, Aug 12, 2008 at 3:26 PM, Christian Fufezan <[EMAIL PROTECTED]> wrote: > Ok, > > "pdb2gmx .... < inter.txt" did the trick. Although it was a bit painful to > generate the inter.txt in the first instance :) > > Thanks again > > Christian Fufezan > > > Dr. Christian Fufezan > Westfälische Wilhelms-Universität Münster > Institut für Biochemie und Biotechnologie der Pflanzen (IBBP) > Hindenburgplatz 55 > 48143 Münster - Germany > > Tel: ++49 251 8324791 > Fax: ++49 251 8328371 > Web: http://www.fufezan.net > > On Aug 11, 2008, at 20:33 , Justin A. Lemkul wrote: > >> >> >> Christian Fufezan wrote: >>> >>> Dear gmx users, >>> I am new to MD and working my way through some tutorials. I saw that >>> pdb2gmx has the "-inter" flag which is used to specify which >>> conformers/protonation stats should be used. >>> Is there a way in which this can be automatised ? >>> For example, lets say I have a list.txt >>> .... >>> HIS A 105 -> HISB >>> .... >>> and I would like to use that list for all runs to be used. >> >> Would this be useful: >> >> http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive >> >> Trying to automate this procedure using -inter is probably a lot more work >> than actually interacting with pdb2gmx. If you're happy with the default >> protonation states of all the other titratable sites (check pdb2gmx -h), >> then you can use -his instead, which might de-complicate things. Otherwise, >> you have to know the order of all the interactively selected residues, which >> protonation state to give them, and how many of each you have. >> >> -Justin >> >>> Thanks in Advance >>> Christian Fufezan >>> _______________________________________________ >>> 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 thewww >>> 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 >> jalemkul[at]vt.edu | (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 > > _______________________________________________ > 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 thewww interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
titratable.sh
Description: Bourne shell script
gmxquery.sh
Description: Bourne shell script
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