Hi,
I asked previously about an error in running production with restraint. After adding -ref flag my job started running perfectly fine. After completing NSTEP = 10000, it terminates and starts second job. My nohup.out file is pasted below,
Starting Script at: Fri Aug 5 21:10:44 PKT 2016
Job 1 started at: Fri Aug 5 21:10:44 PKT 2016
-x: Command not found.
gzip: md_simulation1.mdcrd: No such file or directory
Job 1 finished at: Fri Aug 5 21:32:44 PKT 2016
Job 2 started at: Fri Aug 5 21:32:44 PKT 2016
What is the reason of this strange error.
Thanking you. Best Regards, Saman Yousuf AliJunior Research Fellow,
On Friday, August 5, 2016 1:54 AM, Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
Dear Zoran,
Thank you for helping me to resolve this problem. After adding -ref falg, my job starts running perfectly. I have another query, I want to use the same script with ibelly option. My input is pasted bellow.
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ibelly = 1,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 2500000, dt = 0.002,
ntpr = 1000, ntwx = 500, ntwr = 1000
bellymask = ':',
/
My target total residues are 1-534, cofactor and ligand 535-538, counter ions 539-550 and water molecules (TIP3P box) 551-19480. I want to freeze 268-532 residues. I am confused, how I assign moving residues for bellymask.request you to kindly suggest solution to my problem.
Thanking you.
Best Regards, Saman Yousuf AliJunior Research Fellow,
On Friday, August 5, 2016 12:14 AM, zoran matovic <
zmatovic.kg.ac.rs> wrote:
Hi,You haven’t red our answers carefully. Again u missed to provide reference structure using flag –ref following with usually the same restart file used for –c flag. In your case u should write down additional flag: –ref md_simulation$MDINPUT.rst Cheers Zoran #yiv9232336429 -- filtered {panose-1:2 4 5 3 5 4 6 3 2 4;}#yiv9232336429 filtered {font-family:calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv9232336429 p.yiv9232336429msonormal, #yiv9232336429 li.yiv9232336429msonormal, #yiv9232336429 div.yiv9232336429msonormal {margin-top:0cm;margin-right:0cm;margin-bottom:8.0pt;margin-left:0cm;line-height:107%;font-size:11.0pt;}#yiv9232336429 .yiv9232336429msochpdefault {}#yiv9232336429 .yiv9232336429msopapdefault {margin-bottom:8.0pt;line-height:107%;}#yiv9232336429 filtered {margin:70.85pt 70.85pt 70.85pt 70.85pt;}#yiv9232336429 div.yiv9232336429wordsection1 {}#yiv9232336429 A true friend is someone who is there foryou when he'd rather be anywhere else. -- Len Wein Dr Zoran D. Matović, professor of chemistryDepartment of ChemistryFaculty of ScienceUniversity of Kragujevac34000 KragujevacSerbia Tel/Fax + 381 34 336 223 / 381 34 335 040 From: Saman Yousuf ali Sent: Friday, August 5, 2016 6:18 AMTo: zoran matovic ; Daniel Roe ; AMBER Mailing List Subject: Re: [AMBER] error running production with restraint. Dear Zoran and Daniel,
Thank your for your answer. I have used to following command to run input file
#!/bin/csh
set AMBERHOME="/usr/local/amber14"
set MDSTARTJOB=1
set MDENDJOB=5
set MDCURRENTJOB=$MDSTARTJOB
set MDINPUT=0
echo -n "Starting Script at: "
date
echo ""
while ( $MDCURRENTJOB <= $MDENDJOB )
echo -n "Job $MDCURRENTJOB started at: "
date
. MDINPUT = $MDCURRENTJOB - 1
mpirun -np 8 -machinefile /etc/mpich/machines.LINUX $AMBERHOME/bin/sander.MPI -O -i md_simulation.in \
-o md_simulation$MDCURRENTJOB.out \
-p complex.prmtop \
-c md_simulation$MDINPUT.rst \
-r md_simulation$MDCURRENTJOB.rst \
-x md_simulation$MDCURRENTJOB.mdcrd \
-e md_simulation$MDCURRENTJOB.mden
gzip -9 -v md_simulation$MDCURRENTJOB.mdcrd
echo -n "Job $MDCURRENTJOB finished at: "
date
. MDCURRENTJOB = $MDCURRENTJOB + 1
end
echo "ALL DONE"
but i failed again and got same error. Kindly help me to figure out the reason of this error.
Thanks in advance.
Best Regards, Saman Yousuf Ali
On Thursday, August 4, 2016 11:28 AM, zoran matovic <
zmatovic.kg.ac.rs> wrote:
Hi,
I do not think that your input file is the reason for the run being failed.
You should check if u supplied appropriate restart file ("-c
md_simulation1.rst") and reference file ("-refc file_name.rst(or crd) on the
command line.
Cheers
Zoran
-----Original Message-----
From: Saman Yousuf ali
Sent: Thursday, August 4, 2016 7:16 AM
To: AMBER Mailing List
Subject: [AMBER] error running production with restraint.
Dear all,
After minimization and equilibration steps using amber14 package, I want to
run 5ns production by applying restraint on some part (268-532 residues) of
my target protein, total residues 1-532 residues. I have used the following
input file:
polyA-polyT 10-mer: 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 1,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 2500000, dt = 0.002,
ntpr = 1000, ntwx = 500, ntwr = 1000
restraintmask = ':
268-532.CA,C,N', restraint_wt = 5.0, /
I got this error,
Starting Script at: Thu Aug 4 17:58:27 PKT 2016
Job 1 started at: Thu Aug 4 17:58:27 PKT 2016
Unit 10 Error on OPEN: refc
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
gzip: md_simulation1.mdcrd: No such file or directory
Job 1 finished at: Thu Aug 4 17:58:28 PKT 2016
Job 2 started at: Thu Aug 4 17:58:28 PKT 2016
Unit 9 Error on OPEN: md_simulation1.rst
Is there any mistake in my input file?
Thanks in advance.
Best Regards, Saman Yousuf Ali
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Received on Fri Aug 05 2016 - 02:30:02 PDT
