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

From: Rohith Mohan <>
Date: Wed, 29 Jul 2015 14:06:47 -0700

>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
>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
>What happens if you visualize your system in VMD (using the original PSF
>file)? Does the structure looked warped?
>Jason M. Swails
>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.

Rohith Mohan
UC Riverside
Ph.D. Graduate Student
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Received on Wed Jul 29 2015 - 14:30:02 PDT
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