AMBER Archive (2006)

Subject: AMBER: (no subject)

From: a a (patd_2_at_hotmail.com)
Date: Tue Aug 15 2006 - 05:13:49 CDT

Dear Sir/Madam,

It is the ptraj file that I used to calculate rmsd,

===============================================
trajin jta.mdcrd
trajout jta_ptraj.mdcrd
rms first out jta_linker_nocenter.rmsfit :436-511,512 time 0.50
================================================

Then I type

====================
ptraj jta.prmtop < jta.ptraj
====================

however, everytime I do the calculation, it ends with the following message,
is it normal or due to some error that I should correct it?

================================================
Processing AMBER trajectory file 1K4T_aCPT4_md2.mdcrd

Set 1 .................................................
Set #50 appears corrupted (
22.681 -8.543 27.3283)

PTRAJ: Successfully read in 49 sets and processed 49 sets.
       Dumping accumulated results (if any)

PTRAJ RMS: dumping RMSd vs time data
================================================

Best regards,

Ann

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