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

From: Rohith Mohan <>
Date: Thu, 30 Jul 2015 13:06:11 -0700

I didn't see a warning about ATOMS_PER_MOLECULE so I think the PSF and
Amber files should be compatible. I generated a chamber-free topology using
cpptraj and visualizing in VMD still resulted in a warped image.

While comparing the coordinates from the inpcrd file and the NAMD PDB file
I noticed that for several coordinates there was a mismatch in the sign of
a coordinate. For example, -23.667 -13.159-150.455 from the PDB becomes
-23.6670000 -13.1590000 150.4550000. -150.455 becomes 150.455 which results
in the structure being warped I believe. Additionally in some cases there's
a lack of space between coordinates so I wonder if that may affecting the
structure as well when AMBER reads it e.g: -95.272-102.260-121.094 from the
PDB becomes -95.2720000-102.2600000 121.0940000 in the .inpcrd file.

Rohith Mohan
UC Riverside
Ph.D. Graduate Student

On Wed, Jul 29, 2015 at 6:30 PM, Jason Swails <>

> 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
> incompatible.
> 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?
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Jul 30 2015 - 13:30:02 PDT
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