From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue Sep 05 2006 - 08:15:18 CDT
Dear Jim,
as I mentioned before, I am using CHARMM27, not CHARMM31 parameter
files. Does your advice for TIP3 also applies in this case?
> 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.
In my system I already have TIP3 generated with noangle nodihedral.
Since I needed to add some more water to it I used the solvate plugin on
vmd. I found that the newly added TIP3 molecules have angles
information. This is the topology for 1 TIP3 on wat.psf
!NATOM
1 QQQ 1 TIP3 OH2 OT -0.834000 15.9994 0
2 QQQ 1 TIP3 H1 HT 0.417000 1.0080 0
3 QQQ 1 TIP3 H2 HT 0.417000 1.0080 0
!NBOND: bonds
1 2 1 3
!NTHETA: angles
2 1 3 2 1 3
0 !NPHI: dihedrals
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
It looks like the H-H bond has been removed and angles have been
included (twice?).
So now I have two kind of water, ie, with and without angles, on my
system. How may I regenarate angles (or remove them) for all the waters
to be the same on my psf file?.
At last, I have now noticed that in the topology file distributed with
vmd, H-H bond has already been removed:
RESI TIP3 0.000 ! tip3p water model, generate using noangle
nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
Regards
Cesar
Jim Phillips escribió:
>
> 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
>>>>
>>>
>>
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