----- Original Message ----- From: Mark Abraham <[email protected]> Date: Friday, June 4, 2010 11:51 Subject: Re: [gmx-users] Creation of a Non-Standard Residue To: Discussion list for GROMACS users <[email protected]>
> > > ----- Original Message ----- > From: Mark Zottola <[email protected]> > Date: Friday, June 4, 2010 10:40 > Subject: Re: [gmx-users] Creation of a Non-Standard Residue > To: Discussion list for GROMACS users <[email protected]> > > > Let me clarify.> > > > I have no problem determining the bond stretching > > or angle bending parameters for HCN. This was a very straightforward task. > > Unit conversion to get those values in a gromacs force field was also a > > non-issue.> > > > The problems I am having are:> > > > 1) How do I > > specify a POLAR hydrogen on a carbon atom? There are polar hydrogens (or > > so it seems) in the gromacs forcei field, but ostensibly they are on > > heteroatoms such as nitrogen or oxyen. Is there a way to force gromacs to > > let a polar hydrogen on a carbon? Perhaps I misinterpreted this the first time. Of course all-atom forcefields have polar hydrogens. It seems your problem is that you can't make PRODRG produce an .itp suitable for ffgmx for HCN, because it assumes H bonded to C is non-polar. If so, then you have a potentially tricky problem and need to consult the documentation of that tool. Such a problem exists before GROMACS gets involved, so your second question seems misformed - GROMACS will do whatever you tell it, if that is consistent with the force field you're using. Mark > ffgmx has been deprecated for years (as pdb2gmx tells users), so you'll find > it hard to interest people with this problem. PRODRG beta works for one of > the GROMOS forcefields, however. The general issue is that you're trying to > develop an all-atom model, so you need to target an all-atom forcefield. > > > 2) I AM looking for advice on the van der Waals parameters. Yes, I can > guess and tweak until the cows come home, but obviously there are > recommendations which I do not know. So... any suggestions on this.> > > > > 3) The problem is quite simple, I want to develop parameters for HCN so I > can use it as both ligand AND as a component n a solvent box. I do have the > formula (4 or 5 steps from the web) to create my solvent box, but I need to > have HCN properly parameterized. > > > > 4) I am asking for this as I > cannot use the Dundee server to make the appropriate topology file.> > > > > The warning blurb was good at saying "Parameter development is done by > professionals, so please do not try this at home." I am asking for help in > the above issues as I am new to GROMACS but NOT other MD programs.> > Well, then you'll know how to follow up on the concrete advice there - start > by reading the literature for the force field of interest to see how VDW > parameters were derived. How best to follow up is strongly problem- and > forcefield-dependent. You might decide the path of least resistance is to use > an AMBER forcefield in GROMACS so that you can use AMBERTools automated > parameterization tools. > > Mark > -- > 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
-- 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
