> Hello > I am parametrizing an unnatural amino acid, phenylglycine (PHG), in > the OPLS FF in GROMACS. I have put in the necessary parameters in > the .hdb, .rtp, and the aminoacids.dat file. > 1. When I do grompp for the EM, I get an error saying that I have not > put in the appropriate parameters for the bonds, angles and > dihedrals.
Well that means you haven't done it :-) Go back and compare what you've done for PHG with other amino acids, see what is different and fix it. > Surprisingly, when I do put in the parameters (from the > ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more > distorted, a counterintuitive observation. In fact the simulation is > much better off when I ignore the warnings and the program puts in > zeros after the required parameters in the .top file. Why is this > happening? You can't tell that your force field is a reasonable physical model by looking at the results on their own - you need a comparison with experiment. Often you can tell by looking at the results that it is completely wrong, however. Just putting in zeroes guarantees you a spurious model, whether you can recognise that from the results or not. > Another question related to this: > 2. When I do parametrize a single peptide with a single PHG residue > and then simulate it (with zeros for the parameters in the .top > file), the PHG turns out fine and does not get distorted. But when I > simulate many PHG containing peptides, say 10 of them stacked on top > of and besides each other, I observe that some of the PHGs get > distorted while others don't. By distorted, I especially mean the > Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from > its normal value of about 109. Whatever the cause for this distortion > is, why is it affecting only some PHG residues and not others? It's a stochastic system... run it for long enough and you'll see weird stuff everywhere. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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