AMBER Archive (2008)

Subject: RE: AMBER: 1.5ns rst file to PDB file Conversion Error

From: Ross Walker (
Date: Wed Jul 23 2008 - 04:08:46 CDT

Hi Khuram,


I didn't see the prmtop and rst file attached so can't look at it here.
However, my suspicion is that your rst file has *'s in it somewhere because
an atom has moved too far from the central box and thus it's coordinates are
too large to fit in the space defined for it in the rst file. This normally
takes at least 50ns of MD though for a explicit solvent simulation and for
an implicit solvent simulation it should not occur, assuming you did not
turn off the removal of center of mass rotation and translation (nscm=0).


You may want to visualize your trajectory file and make sure nothing is
flying off at high speed due to some initial VDW clash for example.


A way around this issue is to go back to the previous 'good' restart file
and have ptraj image it for you and then continue the run from there.
Alternatively you can set iwrap=1 in the &cntrl namelist of the mdin file to
make sander always wrap molecules as they translate out of the central box.


If you don't find *'s in your rst file then please send it and we can try
looking at it.


All the best



From: [] On Behalf Of
khuram sb
Sent: Tuesday, July 22, 2008 10:07 PM
Subject: AMBER: 1.5ns rst file to PDB file Conversion Error



I am working with amber 9.
My a_md2_1500ps.rst file is not being converted to pdb file after 1.5ns MD
The following error is generated when I write the following command.

  Command is : ambpdb -p a_charges.prmtop <a_md2_1500ps.rst> ab_md2.pdb

  Error is :
  | New format PARM file being parsed.
  | Version = 1.000 Date = 07/02/08 Time = 04:30:41
  forrtl: severe (64): input conversion error, unit 5, file stdin
  Image PC Routine Line

 The required prmtop and a_md2_1500ps.rst files are also attached here.
 Please any point out the error.
Khuram SB


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