Since you have ntpr=1, are any steps printed in the .out? If so, please
paste a few here.
Bill
On 2/10/16 11:34 PM, Saman Yousuf ali wrote:
> 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 - 00:00:04 PST
