AMBER Archive (2004)

Subject: RE: AMBER: md problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 16 2004 - 09:43:19 CDT

Dear Volodya,
 
I cannot immediately see anything wrong with your input file but sometimes
email formatting can hide underlying formatting errors. The error message
also does not make it clear what unit number the read error occured on. Thus
it could be a read error with the prmtop or inpcrd file. Could you please
post me (as attachments) your inpcrd, prmtop and input files and I'll try it
out on my machine and see if I can see what is wrong. Also, what version of
Amber are you using?
 
All the best
Ross
 
/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Volodymyr Zloy
Sent: 15 September 2004 09:03
To: amber_at_scripps.edu
Subject: AMBER: md problem

Dear Amber users,

 

I have input file for md simulation.

 

molecular dynamics run
 &cntrl
    imin=0,irest=0, ntx=1, tempi=0.,
    scee=1.2, cut=9.0,
    ntt=1, temp0=50.0, tautp=0.2,
    ntp=1, taup=0.2, npscal=1,
    ntb=2, ntc=2, ntf=2, nsnb=25,
    nstlim=500, iwrap=1,
    ntwe=100, ntwx=100, ntpr=25,
    ntr=1,
 &end
Restrained solute
 50.0
FIND
* * * *
SEARCH
RES 1 436
END
END
eof

Unfortunatly, It doesn't work. I have in log file next:

 

fmt: read unexpected character
apparent state: internal I/O
last format: (i5)
lately reading sequential formatted internal IO

What can you reccomend me?

 

Volodya

  _____

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