AMBER Archive (1999)

Subject: mdcrd and ptraj

From: Marcela Madrid (mmadrid_at_gardel.psc.edu)
Date: Wed Nov 17 1999 - 16:11:12 CST

Hi,

I am using ptraj to strip the waters off a trajectory,
and write a new trajectory "stripped",
then I use carnal to read the pdb files from the stripped trajectory.
I think something must be wrong because one of the pdb files that
I get consists of unconnected dots. I do not have this problem
if I use a restrt file instead of the mdcrd.
Did anybody have this kind of experience?

This is the message from carnal:
stream: opening pme66_strip.mdcrd
starting new coord output file: fittopdb.2
starting new coord output file: fittopdb.3
starting new coord output file: fittopdb.4
(EOF reached on pme66_strip.mdcrd)
incomplete coord set: pme66_strip.mdcrd (3 atoms out of 17494):
        starting another file if any
STREAM s1: no more files/crds (iteration 4)

I expect 3 pdb files of 17494 atoms each.
Any ideas? thanks, marcela