Re: Acetaldehyde Dihedral Parameters

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 06 2007 - 14:28:20 CDT

Well, you could *put* a dihedral there; you'd just expect it to have a
period of 120 degrees and a fairly low force constant.
Peter

L. Michel Espinoza-Fonseca wrote:
> 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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