From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Jun 06 2007 - 12:21:38 CDT
That's a good question. I don't think so, I might be wrong. Perhaps
the best thing to do here is to avoid making that dihedral and then
run a short test of the acetaldehyde in water. If things are fine, the
only part of the molecule that should rotate is methyl group.
Anyway, looking at the structure of the molecule, I think that a
dihedral shouldn't be there. I'll try to check it again and write
back.
Michel
2007/6/6, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> Actually... in looking at the topology files, the auto dihedrals is
> being pulled in by the parent topology file (top_all22_prot.inp). Michel
> (or anyone else), do you happen to know if the auto statement is
> supposed to propagate to stream files that are loaded in? If so, that
> dihedral *should* be there, and the parameters are just missing. If not,
> Kevser, you'll need to include "auto none; auto angles" in the segment
> command for generating the acetaldehyde, to avoid making that dihedral:
>
> segment A {
> pdb aald.pdb
> auto none
> auto angles
> first none
> last none
> }
>
> Peter
>
> Peter Freddolino wrote:
> > You may also need to make sure you're *not* using an AUTO DIHEDRALS
> > directive in psfgen, if the acetaldehyde topology isn't designed to have
> > one...
> >
> > Peter
> >
> > L. Michel Espinoza-Fonseca wrote:
> >
> >> That's strange. If you're using acetaldehyde, such "dihedral"
> >> shouldn't exist (Look at the end of the file you're pointing to).
> >> Instead, there should be an improper to keep such "dihedral"
> >> constrained.
> >>
> >> Perhaps you should try to prepare your system again, making sure that
> >> everything looks fine. One more piece of advise: when you use stream
> >> files, you also need to tell psfgen to read a parent file (i.e.,
> >> top_all22_prot.inp).
> >>
> >> Cheers,
> >> Michel
> >>
> >> 2007/6/6, Kevser Göçmen Topal <kevser_at_boun.edu.tr>:
> >>
> >>>
> >>>
> >>>
> >>>
> >>> Hello,
> >>>
> >>>
> >>>
> >>> In the stream file "topar_all22_prot-aldehydes.str" dihedral
> >>> parameters for "aldhyde proton-carbonyl carbon-methyl carbon-methyl
> >>> proton"
> >>> are missing.
> >>>
> >>>
> >>>
> >>> MD run of my system crashes with error message "FATAL ERROR: CAN'T
> >>> FIND DIHEDRAL PARAMETERS FOR HR1 C CT3 HA" .
> >>>
> >>>
> >>>
> >>> Does any one have an idea to deal with this problem?
> >>>
> >>>
> >>>
> >>> Thanks in advance.
> >>>
> >>>
> >>>
> >>> Best regards,
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Kevser Göçmen Topal
> >>>
> >>>
> >>>
>
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