HI Jason,
Here is the input:
Input file for running QM-MM-GBSA (50 frames are used)
&general
startframe=1000, endframe=1100, verbose=1, interval=25
/
&gb
igb=5, saltcon=0.100, ifqnt=1,qm_residues="320; 18-20; 23-27; 43-45; 65-66; 69; 74-77; 88-97; 128; 133; 141-142; 144; 153-156; 177; 298; 301-302",qm_theory="PM3"
/
Here is the running command:
mpiexec MMPBSA.py.MPI -O -use-mdins -i qm-gbsa_egfr.in -o M19_EGFR_MMPBSA_QMGBSA.dat -cp com_m19.top -rp rec_m19.top -lp m19.top -y noWAT_m19_egfr_total_nobox_center.mdcrd
The mdins files are named:
_MMPBSA_gb.mdin
_MMPBSA_gb_qmmm_com.mdin
_MMPBSA_gb_qmmm_lig.mdin
_MMPBSA_gb_qmmm_rec.mdin
When i run only the first file is retained and the rest are deleted and i got this error:
IOError: Input file (_MMPBSA_gb_qmmm_com.mdin) doesn't exist
Error occured on rank 1.
Exiting. All files have been retained.
IOError: Input file (_MMPBSA_gb_qmmm_com.mdin) doesn't exist
Error occured on rank 3.
Exiting. All files have been retained.
IOError: Input file (_MMPBSA_gb_qmmm_com.mdin) doesn't exist
Is it possible to rename the inputs and supply the names explicitly in the script, although i searched the manual but i didn't fine such way. By the way, i tried to remove the -O option but this also didn't work.
In the meantime i will try your way to see if it works...
Thanks in advance
Marawan
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 7 January 2013 10:35 PM
Subject: Re: [AMBER] MMPBSA error
On Mon, Jan 7, 2013 at 5:44 AM, marawan hussain <marawanhussain.yahoo.com> wrote:
Hi Jason,
>Thanks a lot for your answer.
>I tried to use other machine that has a correct installation although i have a very limited quota on it just to see how the QM/MM binding energy goes on.
>I want to use the dispersion corrected AM1 "AM1-D*" option via the -make-mdins and the -use-mdins- regime..I'm noticing that once the new job starts it deletes the input files and give an error unless i quickly recopy the inputs again to the working directory, i tried the "keep_files=2" command but it didn't work..Could you please advice..
>
I cannot reproduce this behavior. Are you renaming the mdin files? Another possibility is that a different command (hidden or not) in your PBS script or environment is purging these files.
Try automating the procedure with a single PBS script running both MMPBSA.py commands (with -make-mdins and -use-mdins), using "sed" to modify the intermediate input file automagically.
In the meantime, I will add AM1-D* as an allowable value for the qm_type variable.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jan 07 2013 - 19:00:03 PST
