Dear Justin. The errors have now gone away once I followed your suggestion of entering the missing parameters directly in the topology file. Though there is no explanation as to why it didn't work with ffbonded.itp, I guess sometimes ignorance is bliss ;)
Thanks again. Cheers Abhishek > > > On 2/14/13 4:15 PM, Abhishek Acharya wrote: >> >> >>> Hello Justin >>> Thank you very much for your effort and help. I will try adding new >>> parameter corresponding to the errors. Meanwhile just out of curiosity >>> and >>> possible need, what should be done in case no matching parameters are >>> found for the missing dihedrals? I see that there are 6 fields in the >>> dihedrals section of ffbonded.itp. How do we calculate these parameters >>> for new dihedrals ? >> >> I wanted to go step by step. I first tried to address the errors 1, 2 >> and >> 3. So I added the following dihedrals to ffbonded.itp. >> >> For Error1: >> HC CT CT NA 3 -4.09614 5.08775 2.96645 >> -3.95806 >> 0.00000 0.00000 >> from: >> HC CT CT NT 3 -4.09614 5.08775 2.96645 >> -3.95806 >> 0.00000 0.00000 ; amine all-atom >> >> For Error2 >> OH CT CT NA 3 9.89307 -4.71746 3.67774 >> -8.85335 >> 0.00000 0.00000 >> from: >> N3 CT_2 CT OH 3 9.89307 -4.71746 3.67774 >> -8.85335 >> 0.00000 0.00000 ; Chi for Ser & Thr >> >> For Error3 >> CT OS CT NA 3 -5.23000 7.32200 6.27600 >> -8.36800 >> 0.00000 0.00000 >> from: >> CT OS CT N 3 -5.23000 7.32200 6.27600 >> -8.36800 >> 0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines >> >> I expected this to remove the errors 1, 2 and 3. I took care to keep the >> atomtypes order the same. But this doesn't seem to affect the result. I >> get the same errors. Any ideas?? >> > > None. If you add new parameters in the right directive, the errors will > go > away. I can offer no explanation as to why that's failing here. You can, > of > course, enter all the missing parameters directly into the topology rather > than > having them looked up from ffbonded.itp, but that really shouldn't be > necessary. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
