Thanks for your reply Dave. I apologize for maybe not having explained things very well.
This is what I run:
minimization:
/usr/local/amber11/bin/pmemd -O -i min1.in -o TSL2_1N8R.wat.min1.out -inf TSL2_1N8R.inf -c TSL2_1N8R.wat.crd -ref TSL2_1N8R.wat.crd -r TSL2_1N8R.wat.min1 -p TSL2_1N8R.wat.top -x TSL2_1N8R.wat.min1.x -e TSL2_1N8R.wat.min1.ene
/usr/local/amber11/bin/pmemd -O -i min2.in -o TSL2_1N8R.wat.min2.out -inf TSL2_1N8R.inf -c TSL2_1N8R.wat.min1 -ref TSL2_1N8R.wat.min1 -r TSL2_1N8R.wat.min2 -p TSL2_1N8R.wat.top -x TSL2_1N8R.wat.min2.x -e TSL2_1N8R.wat.min2.ene
equilibration:
/usr/local/amber11/bin/pmemd -O -i md1.in -o TSL2_1N8R.wat.md1.out -inf TSL2_1N8R.inf -c TSL2_1N8R.wat.min2 -ref TSL2_1N8R.wat.min2 -r TSL2_1N8R.wat.md1 -p TSL2_1N8R.wat.top -x TSL2_1N8R.wat.md1.x -e TSL2_1N8R.wat.md1.ene
etc to md19 (so in total, 2x minimization + 19x equilibration)
where the .in files min1.in, min2.in and md1.in (etc) are the ones I copied here yesterday.
TSL2_1N8R.wat.min1, the file that is blank (ie, empty) is generated by pmemd in the first minimization round, but pmemd gives me a TSL2_1N8R.wat.min1 that is empty. To my poor understanding, TSL2_1N8R.wat.min1 is the restart file for the next step of the minimization, and thats why TSL2_1N8R.wat.min2 (the next restart file) is not generated, so pmemd aborts. Also, TSL2_1N8R.wat.min1.out is generated with results in it, but TSL2_1N8R.wat.min2.out has no results.
To generate TSL2_1N8R.wat.min1, in principle I only need TSL2_1N8R.wat.crd, TSL2_1N8R.wat.top and min1.in, which are all in the right directory and with the right names. Basically, what I've done is duplicate an old directory where I run this same minimization/equilibration in the past, and try to run the same files again with the new compilation. I haven't changed any names, that's why I dont understand what's wrong. Also, I haven't only duplicated one directory, I've duplicated 3 directories of 3 different old minimizations. None of the three share any files (not even the scripts), they are all independent, but they all give me this error.
I know it sounds like something very basic, I apologize. I guess my question is, what can I test to figure out why TSL2_1N8R.wat.min1 is empty? I really tried to run this many times before coming here...
Also, I forgot to say this is all in CPU.
Thanks very much again,
Amparo
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 07 June 2013 18:01
To: AMBER Mailing List
Subject: Re: [AMBER] unable to run minimizations after new installation of amber11
On Thu, Jun 06, 2013, Amparo Garcia Lopez wrote:
> At line 109 of file inpcrd_dat.f90 (unit = 9, file = 'TSL2_1N8R.wat.min1')
> Fortran runtime error: End of file
>
> The file TSL2_1N8R.wat.min1 is in blank.
Since TSL2_1N8R.wat.min1 is an input file, and is blank (empty?), it makes
sense that pmemd would complain about a premature end of file.
> Unit 9 Error on OPEN: TSL2_1N8R.wat.min2
> STOP PMEMD Terminated Abnormally!
This looks like you may be trying to open an non-existent file? Is that
possible?
The inputs you sent are not very helpful...what is important here are the file
names you are giving to pmemd on the command line...these are printed in
the output file. I'm guessing that all this has nothing to do with having a
new version of Amber, but involves problems with finding the same files you
used to use.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 07 2013 - 10:00:02 PDT
