Re: Minimization messes up C terminal

From: Victor Ovchinnikov (ovchinnv_at_mit.edu)
Date: Sat Jun 26 2010 - 09:07:45 CDT

Can you try 'generate protein first nter last cter setup warn' in your
generate command (assuming your n-terminal is regular)? Peter's
suggestion to use 'AUTOGEN ANGL DIHE' should also work if you add
patches after generating the segment. If both of these ways won't work,
there is something quite wrong happening elsewhere.
Regards,
Victor

On Fri, 2010-06-25 at 21:02 -0400, Peter Freddolino wrote:
> Hi Pavan,
> My knowledge of using charmm to generate structure files is quite
> limited. Is there any reason you're not using namd's psfgen? Did you
> try calling autogen
> (http://www.charmm.org/documentation/c34b1/struct.html#%20Autogen)
> after applying the terminal patches?
> Editing things by hand is almost never the right answer; given that
> people regularly use charmm with cmap, I have to assume that there is
> some command to generate the needed angles/dihedrals, so if they are
> indeed missing from the psf, you should probably check on the charmm
> forums and see what the correct solution is.
> Best,
> Peter
>
>
> On 06/25/2010 10:19 AM, Pavan G wrote:
> > Hello Peter,
> > I tried regenerating angles and dihedrals with the Charmm script
> > using the 'generate protein setup' command but it didn't add the
> > terminal OT1--C--OT2 angle and relevant dihedrals. So I manually
> > added them in to the PSF file. This fixed the problem in the sense
> > that I managed to heat the system (npt) to 400K w/o crashing. But
> > now when I look at the output file, the pressure lines are all 0's.
> > PRESSURE: 1000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 2000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 3000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 4000 0 0 0 0 0 0 0 0 0
> > .........
> > PRESSURE: 77000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 78000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 79000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 80000 0 0 0 0 0 0 0 0 0
> > PRESSURE: 81000 0 0 0 0 0 0 0 0 0
> >
> > Could the manual addition of angles and dihedrals be the reason
> > behind this behavior? The trajectory looks fine though. The RMSD
> > increases as the temperature is increased. In fact if I don't look
> > at the output file everything looks fine :)
> > Any comments are greatly appreciated.
> > Pavan
> >
> > On Wed, Jun 16, 2010 at 12:48 PM, Peter Freddolino
> > <petefred_at_ks.uiuc.edu> wrote:
> > Hi Pavan,
> > this usually happens if you use a CMAP topology file but do
> > not
> > regenerate angles and dihedrals after psf generation. It
> > would help if
> > you could post the name of the topology file that you're
> > using, and the
> > version of vmd.
> > Best,
> > Peter
> >
> > On 06/16/2010 11:32 AM, Pavan G wrote:
> > > Hello All,
> > > I am trying to run a NAMD simulation of a protein in water
> > with
> > > Charmm27 ff. The terminal carboxyl carbon and two oxygens
> > look fine in
> > > the starting structure but as soon as the minimization
> > starts the two
> > > oxygens come close to each other and the simulation fails
> > later when I
> > > start NVT and/or heat beyond 250K. The charges on the
> > oxygens are
> > > -0.67 each and charge on carboxyl carbon is 0.34 as
> > expected. I fail
> > > to see why minimization would force two highly (both
> > negative) charged
> > > atoms close to each other. Any help would be appreciated.
> > The C
> > > terminal residue was created with the cter patch in
> > Charmm.
> > > Thanks,
> > > Pavan
> > >
> >
> >

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