Re: [AMBER] Issues with running simulation after ParmEd conversion

From: Jason Swails <>
Date: Wed, 29 Jul 2015 21:30:26 -0400

On Wed, Jul 29, 2015 at 5:06 PM, Rohith Mohan <> wrote:

> >I don't think that the size of the system should really impact things
> >here (outside of perhaps taking a few minutes to process completely).
> >What I've usually had the most trouble with in terms of chamber
> >conversion has been the unit cell definition.
> >
> >Unlike Amber, CHARMM doesn't store the unit cell vectors or dimensions
> >in the coordinate files or the PSF (I'm actually not sure where that box
> >information is stored for restarting simulations with a barostat). So I
> >suspect what's happening here is that the unit cell dimensions are not
> >being set correctly for your system. Does your PDB file define a CRYST1
> >record? If so, where did those values come from? If not, then you are
> >missing unit cell information and it doesn't seem to be getting set
> >anywhere.
> >
> >If you are using NAMD, then I think it prints an XST file or something
> >like that that defines unit cell vectors. Have you made sure to convert
> >those unit cell vectors to the appropriate tuple of vector lengths and
> >angles?
> >
> >What happens if you visualize your system in VMD (using the original PSF
> >file)? Does the structure looked warped?
> >
> >HTH,
> >Jason
> >
> >--
> >Jason M. Swails
> >BioMaPS,
> >Rutgers University
> >Postdoctoral Researcher
> Hello Jason,
> Thanks for your response.
> The PDB file does contain a CRYST1 record which matches up with the unit
> cell values given at the end of the .xst file. ParmEd chamber appears to be
> using the CRYST1 values when generating the .inpcrd file too so I think the
> unit cell definition is being recognized correctly. There's a slight
> discrepancy in the values as there's some rounding involved when generating
> the PDB from the equilibration trajectory
> i.e. 118.04368303 181.984011337 181.984011337 vs CRYST1 118.044 181.984
> 181.984. But even manually editing these values to reflect the original
> exact values from the .xst file doesn't appear to resolve the issue when
> performing the production run.
> When visualizing in VMD, using the original PSF file and the ParmEd
> generated .inpcrd (using the Amber Coordinates with Periodic Box filetype
> designation) the structure does look extremely warped but I wasn't sure if
> it was due to incompatibility of the inpcrd file and the psf.

‚ÄčOK. There are circumstances when ParmEd has to reorder some atoms of the
topology file. Did you see a warning message about ATOMS_PER_MOLECULE
being corrupt? If so, the PSF and Amber coordinate files will be

Try generating a chamber-free topology file using cpptraj and see if
visualizing it with VMD still yields a warped image. The following command
should work:

cpptraj -p your.prmtop << EOF
parmwrite visualization.parm7 nochamber

Just make sure you never use visualization.parm7 for the simulation.

Another possible idea is that the PDB file has coordinates that too large
to fit in the assigned space. If you compare the coordinates from the
inpcrd file and the NAMD coordinate file, do they match?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 29 2015 - 19:00:02 PDT
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