VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Sep 04 2006 - 16:44:44 CDT

The "auto none dihedrals" bit in the membrane plugin output appears to
have been caused by a bug in the psfgen readpsf command. The membranes
are actually build with "auto angles dihedrals", but psfgen was never
reading the angles flag from the psf file comments.

-Jim

On Mon, 4 Sep 2006, Cesar Luis Avila wrote:

> I am using CHARMM 27 parameter files included on VMD:
> vmd/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp
> vmd/plugins/noarch/tcl/readcharmmpar1.0/par_all27_prot_lipid_na.inp
>
> In particular for TIP3 residue there is an explicit indication to generate
> with no angle nor dihedral:
>
> "tip3p water model, generate using noangle nodihedral"
>
> For DMPC there is no explicit indication on topology file, so I suppose that
> one should generate angles and dihedrals. This also applies for POPC. So I
> don't know why membrane builder on VMD uses auto none dihedrals for lipids
> segment. Shouldn't it be auto angles dihedrals? Since dihedrals are generated
> from angles what is the point of using such a command?
>
> Regards
> Cesar
>
> Jim Phillips escribió:
>>
>> The most accurate place would be to look at the topology file itself.
>>
>> My personal advice is to remove the H-H bond from the TIP3 structure and
>> then run "regenerate angles dihedrals" on the whole structure before you
>> write it out. This is required if you're using CHARMM 31 or newer
>> parameter files where the patches no longer include angles and dihedrals.
>>
>> -Jim
>>
>>
>> On Fri, 1 Sep 2006, Cesar Luis Avila wrote:
>>
>>> Where can I find information on when to generate angles and dihedrals for
>>> different segments?
>>> Throughout internet I have found different ways for generating segments
>>>
>>> For water
>>> {first none
>>> last none
>>> auto none }
>>>
>>> According to psfgen manual "Because CHARMM uses an additional H-H bond we
>>> must disable generation of angles and dihedrals for segments containing
>>> waters". Does this apply only to TIP3? What about other water models?
>>>
>>> For membranes :
>>> {first none
>>> last none
>>> auto none dihedrals}
>>>
>>> This options were used by membrane builder on VMD. Does this also apply to
>>> other lipids like DMPC? Why shouldn't angles be generated in this case?
>>>
>>> At last for proteins
>>> {first nter
>>> last cter
>>> auto angles dihedrals}
>>> This options were used by autopsf builder on VMD.
>>>
>>> Any help will be very much appreciated.
>>> Regards
>>> Cesar
>>>
>>
>