Yup. Initially I was just confused on how to parameterize the protein using the MARTINI ff. I thought there was an automatic way to do it using pdb2gmx only to see Gromos force fields available. But now I realize I have to generate the .itp file using the perl script. Anyway, I've got it figured out :). Thanks for your concern though.
On 25 March 2010 19:22, Justin A. Lemkul <[email protected]> wrote: > > > [email protected] wrote: > >> Hi Justin, >> >> I did not mention that I am indeed trying run Gromacs implementing the >> MARTINI force field. I realize this is not as automatic as selecting other >> force fields in Gromacs using pdb2gmx. This issue has been previously >> discussed in: >> >> http://www.mail-archive.com/[email protected]/msg14945.html >> >> > Did you follow the actual tutorial on the MARTINI site? You should not > ever have to invoke pdb2gmx. Topology generation is conducted using > MARTINI-specific scripts. In the future, it will save a lot of time (both > yours and ours) if you provide complete, legitimate information. After all, > you do not want to use Gromos96, but your first post clearly stated that you > were trying to use this force field. If you want free help, make it easy > for us to do so. > > -Justin > > -Lili >> >> On 25 March 2010 18:13, Justin A. Lemkul <[email protected] <mailto: >> [email protected]>> wrote: >> >> >> >> >> [email protected] <mailto:[email protected]> wrote: >> >> Dear GMX users, >> >> I have a quick question regarding which Gromacs force field in >> pdb2gmx is best suited for creating a topology (itp) file for >> the enzyme, lactate oxidase. So far the force fields in Gromacs >> 4.0.4 are: >> >> 0: GROMOS96 43a1 force field >> 1: GROMOS96 43a2 force field (improved alkane dihedrals) >> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) >> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) >> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) >> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) >> 6: [DEPRECATED] Gromacs force field (see manual) >> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR >> 8: Encad all-atom force field, using scaled-down vacuum charges >> 9: Encad all-atom force field, using full solvent charges >> I selected the "G53a6 GROMOS96 53a6 Forcefield" for creating my >> itp file, however, when I try to run grompp to generate the .tpr >> file, I get the error: >> >> ------------------------------------------------------- >> Program grompp_d, VERSION 4.0.4 >> Source code file: toppush.c, line: 947 >> >> Fatal error: >> Atomtype Qd not found >> ------------------------------------------------------- >> >> I've looked into other discussions on this >> (http://www.mail-archive.com/[email protected]/msg15722.html), >> and concluded that the atomtype Qd must not be present in the >> G53a6 force field. My system is simply the protein lactate >> oxidase. Does anyone have suggestions on which force field(s) >> is best suited for this molecule? >> >> >> Since the atom type "Qd" is not present in the 53a6 parameter set, >> this error has nothing to do with the appropriateness of your force >> field choice. Somewhere, you've incorporated a nonsensical atom >> type. The only time I have ever seen "Qd" is in the MARTINI coarse >> grain force fields. Be sure you're using the topologies you think >> you are; if you really are using an unaltered pdb2gmx-generated >> topology for 53a6, there is no way that this atom type would be >> found therein. >> >> -Justin >> >> Thanks in advance, >> Lili >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > http://lists.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 >
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