AMBER Archive (2006)

Subject: Re: AMBER: PTRAJ RMS: dumping RMSd vs time data

From: Adrian Roitberg (
Date: Sat Nov 04 2006 - 07:00:40 CST

Have you checked the file t1eq.rms to see what is in there ? That is
where you asked ptraj to dump the rms data vs time.

r. a. wrote:
> Dear Amber Users
> I heated up my system slowly from 0-375K, when I checked density, pressure,temperature, kinetic & potential , & total energy, it seemed everything is fine with the system during the simulation but when I m sending the trajectory files to ptraj I always have this error: PTRAJ RMS: dumping RMSd vs time data
> my ptraj file is:
> trajin heat4.crd
> trajin eq4.crd
> trajin md4.crd
> rms first out t1eq.rms :1-388_at_CA,C,N
> strip :WAT
> go
> It would be grateful if anyone provide me with some more information about this problem. I checked the amber archive & tried to use that but it wasnt successful.
> Regards

                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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