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 -Lili On 25 March 2010 18:13, Justin A. Lemkul <[email protected]> wrote: > > > [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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== >
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