Dear all,I have tried to run minimization of apo protein. I have prepared topology files using ff14SB force field (amber14). Before running minimization, I checked my structure using cpptraj checkoverlap command to see if atoms are close to other atoms. I have found that protein contain some bad contact because leap added missing atoms then I started running minimization. I got the following error message. Sander runs for few cycles of minimization and stops with following error message (below)> minimization.inrestrain_min
&cntrl
imin = 1,
maxcyc = 500,
ntpr = 1,
ntb = 1,
cut = 10.0
/
Hold the system fixed
25.0
RES 1 541
END
END
> sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd
> "ERROR MESSAGE"
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:
#0 0x33E3419497
#1 0x33E3419ADE
#2 0x36184358EF
#3 0x4D5DB5 in nb_adjust_
#4 0x4D7FE6 in ewald_force_
#5 0x64AFCF in force_
#6 0x484743 in runmin_
#7 0x47132F in sander_
#8 0x46CBBC in MAIN__ at multisander.F90:?
Segmentation fault (core dumped)
then I tried to minimize the same apo protein (with bad contact) via amber12 using ff99SB, minimization run perfectly with out any error message and I have completed all step then check structure again using cpptraj command. I found that after minimzation structure is fine (without any bad contacts). I used the following script for minimization,
>Minimization Amber12
&cntrl
imin=1, maxcyc=1000, ntmin = 2,
ntx = 1, ntc = 1, ntf = 1,
ntb = 1, ntp = 0, ncyc = 100,
ntwx = 1000, ntwe = 0, ntpr = 1000,
ntr = 1, cut = 10.0
&end
Restraints
25.0
RES 1 541
END
END
I want to know that why amber14 minimization failed while amber12 completed all minimization steps without any error message.
Thank you.
Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID:
saman.yousufali64.yahoo.com
saman.ali.iccs.edu
|
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Received on Thu Feb 11 2016 - 00:00:03 PST
