From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jun 25 2010 - 20:02:41 CDT
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 <mailto: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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