Re: [AMBER] cpptraj not processing all mdcrd files

From: Daniel Roe <>
Date: Fri, 25 Jul 2014 10:25:50 -0600


On Thu, Jul 24, 2014 at 3:50 PM, Kshatresh Dutta Dubey <>

> [trajin ../SF-com-run4.mdcrd]
> Reading '../SF-com-run4.mdcrd' as Amber Trajectory
> Warning: SF-com-run4.mdcrd: Could not accurately predict # frames.
> This usually
> Warning: indicates a corrupted trajectory or trajectory/topology
> Warning: mismatch. Will attempt to read 1702 frames.
> [lie :440 :1-439 out lie-SF.dat]

If you are receiving this message for 'SF-com-run4.mdcrd' but not any of
the other trajectories, that indicates that the trajectory is not being
read properly.

> Please help me figure out the problem. Same trajectories runs fine for RMSF
> and RMSD calculations as well as vmd.

Do you mean that you can read in 'SF-com-run4.mdcrd' sometimes but not
others? Are you sure you are using the same topology? I think as a first
step if you could post your entire cpptraj output for a run that doesn't
work for you and a run that does work for you that will help to figure out
what exactly you are running.


> Thanks in advance
> Regards
> Kshatresh
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Fri Jul 25 2014 - 09:30:03 PDT
Custom Search