AMBER Archive (2006)

Subject: Re: AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly...

From: fine wu (finewu_at_gmail.com)
Date: Thu Jul 20 2006 - 10:55:55 CDT

2006/3/31, Thomas E. Cheatham, III <cheatham_at_chpc.utah.edu>:
>
>
> > I am a novice of Amber and wondering if anyone can help me with this
> > problem. It is a simple task to try to convert a list of Amber restart
> > files to PDB format files using ptraj command. The OS is Linux
> (cluster)
> > and it is Amber version 7. According to the manual the second argument
> ...
> > ERROR in readParm: ...failed to find CHARGE
> >
> > But when I opened the topology file, apparently there are charges
> section in
> > that file:
> >
> > %FLAG
> > CHARGE
> > %FORMAT(5E16.8)
>
> This should work, but obviously is hiccuping if you are seeing this
> problem. You could try getting the ptraj version of the WWW site (which
> is out of date, but more bug fixed than AMBER7):
>
> http://www.chpc.utah.edu/~cheatham/software.html
>
> Two issues come to mind:
>
> (1) ptraj is not properly handling the non-determinant order of the
> parameters (a bug in the older versions) or
>
> (2) the file was moved from a windows box or to a windows box? If you
> did this, there can be extra carriage returns in addition to newline
> characters at the ends of lines which confuses earlier versions of ptraj.
> You could detect this by doing (on Unix/Linux) od -c prmtop and looking
> for \r\n at the end of the lines. The \r can be removed by an editor or a
> newer version of ptraj can be used.
>
>
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Thank you very much for the help. However, there is no carriage return
characters added, only \n there when I checked with od -c command. It seems
working in amber 8 at first but all the waters weren't stripped even "strip
:WAT" was applied in the script or through command line.

The prompt output under amber 7 is like this:

[user_at_server root]$ ptraj
Input the name of an AMBER prmtop or CHARMM PSF:
prmtop
Opened file prmtop with mode (r)
Read in control variables
Read in atom names...

ERROR in readParm: ...failed to find CHARGE

[user_at_server root]$
--------------------------------------------------------------------------------------
The prompt output under amber 8 is:

[user_at_server root]$ ptraj

Input the name of an AMBER prmtop or CHARMM PSF:
prmtop

Opened file prmtop with mode (r)
 MET VAL ASP MET MET ASP LEU PRO ARG SER
 ARG ILE ASN ALA GLY MET LEU ALA GLN PHE
ILE ASP LYS PRO VAL CYS PHE VAL GLY ARG
  LEU GLU LYS ILE HID PRO THR GLY LYS MET
PH E IL E LE U SE R AS P GL Y GL U GL Y LY S AS
 N GL Y TH R IL E GL U LE U ME T GL U PR O LE U AS
G LU G LU I LE S ER G LY I LE V AL G LU V AL V
 AL G LY A RG V AL T HR A LA L YS A LA T HR I LE L
 CYS THR SER TYR VAL GLN PHE LYS GLU
 ASP SER HID PRO PHE ASP LEU GLY LEU TYR
GLU ALA VAL LYS ILE ILE HID ASP PHE
  PRO GLN PHE TYR PRO LEU GLY ILE VAL GLN
AS P ME T TR P AS N SE R GL Y PH E GL U SE
 R TY R GL Y SE R SE R SE R TY R GL Y GL Y AL A GL
T YR T HR G LN S ER P RO G LY G LY P HE G
 LY S ER P RO A LA P RO S ER G LN A LA G LU L YS L
 ARG ALA ARG ALA GLN HID ILE VAL
..........
  ASP TYR ARG GLU TYR GLY ARG ARG LEU VAL
IL E AR G AR G SE R AL A LE U ME T WA
 T WA T WA T WA T WA T WA T WA T WA T WA T WA T WA
W AT W AT W AT W AT W AT W AT W AT W
 AT W AT W AT W AT W AT W AT W AT W AT W AT W AT W
 WAT WAT WAT WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT
  WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
WA T WA T WA T WA T WA T WA T WA
 T WA T WA T WA T WA T WA T WA T WA T WA T WA T WA
W AT W AT W AT W AT W AT W AT W
 AT W AT W AT W AT W AT W AT W AT W AT W AT W AT W
 WAT WAT WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
.................

So it seems every 30 ~40 AA residue or WATER molecules, their names are
extracted strangely from the prmtop file. I never had this kind problem
when deal with other prmtop/restrt/mdcrd files in the Unix or cluster
system. Only these files which has been transferred from cluster to PC for
DVD storage and now transfer back for conversion.
Is there any chance the file was altered during the storage process? If
anyone has a clue about this that will be great.

--Fine

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