In my previous message I used "all-atom" in stead of "united-atom" twice: in the part about the SDS topology and again between the parentheses in my third question. That's probably very confusing, so I made the corrections in my quoted message below. Sorry for the inconvenience.
Louic > Hi everybody, > > I want to do a refinement of an NMR structure, using NOE restraints. I > want to do this in SDS, using an SDS topology file[1] that was designed > for gromacs, but there are no explicit hydrogen atoms. I think it's not > a good idea to simulate a peptide with explicit hydrogens in combination > with an *united*-atom SDS topology (correct me if I'm wrong). If I understood > correctly from a previous (different) question[2], virtual interaction > sites can be used instead of hydrogen atoms to define NOE restraints. > > Now all I need to do is calculate the positions of these sites. I > thought it might be a good idea to use the "protonate" command on the > input structure of my peptide (.gro) and calculate the position of a new > virtual interaction site for the NOE constraint. This new virtual atom > would have be positioned relative to the atoms that are available in the > gromacs all-atom forcefield because it will be added to the > non-protonated input file. > > I tried to use "pdb2gmx -vsite hydrogens" command, but it either: > - does not seem to recognise the atom types of the protonated input > structure because I select the ffG43a1 forcefield for the output file. > - creates only virtual interaction sites on my LYSH residues in a > non-protonated input file because they are the only ones in my peptide > that still contain protons in ffG43a1. > This behaviour seems normal to me, but let me know if I'm missing > something here. Maybe I'm not using pdb2gmx the right way? (more > information below[3] ) > > > My questions are: > - Can pdb2gmx generate the virtual interaction sites for me? How? And if > not: > - Is the procedure described above correct, or is there a better way? > - Does a script/program to calculate virtual interaction sites based > on amino-acid protons already exist? I'm capable of writing one > myself, but since it takes time I only want to do that if nothing > is available already. > - Am I correctly assuming that I would add a non-charged virtual > interaction site without a mass (so only a position to define the > restraint because the proton mass and charge are already accounted > for in the *united*-atom forcefield) > > > Thanks beforehand, I'm looking forward to my "mdrun"... > > Louic Vermeer > IPBS / CNRS, Toulouse > Wageningen University, Wageningen > > > -- footnotes below -- > > [1] http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml > [2] http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ > > [3] > > - starting from a pdb-file containing "pseudo atoms" > # pdb2gmx -f input.pdb -o output.pdb -inter -ignh - vsite hydrogens > Fatal error: > Atom QB in residue LYSH 1 not found in rtp entry with 13 atoms > while sorting atoms > > - starting from a protonated file without the pseudo atoms: > # pdb2gmx -f input.pdb -o output.pdb -inter - vsite hydrogens -ignh > No error, but only LYSH gets virtual interaction sites. Removing the > "-ignh" leads to an error again: Atom "HA" not found in residue LYSH. > > > -- end -- > _______________________________________________ > 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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
