Thank you for the reply. In that case, would the solvation energy be
calculated?? Incase we use dried trajectories, would it generate any
issues? And could you please tep what would be the differences if we use a
solvated trajectory and a dried trajectory?
Regards,
Sruthi
On Sat, 15 Jan 2022 at 12:39 PM, ABDUL BASIT <abdul48_sit.jnu.ac.in> wrote:
> Please use only dried trajectories.
>
> On Sat, Jan 15, 2022 at 3:27 AM Sruthi Sudhakar <
> sruthisudhakarraji.gmail.com> wrote:
>
>> Dear all,
>>
>> I am trying to do MMPBSA calculation on a trajectory with 2:1 binding of
>> ligands on a receptor. I want to get the energy calculations for all 2
>> ligands separately and the system with ligands together. To do this, I
>> have
>> done the following strategy:
>> 1. Created 2 different nc files from the final production.nc by stripping
>> out 1 ligand each
>> 2. Generated the corresponding prmtop files by stripping atoms using
>> ante-MMPBSA.py (for dry complex)
>>
>> But upon running mmpbsa in this system, the following error popped up.
>>
>> *Preparing trajectories for simulation...
>> *
>> *Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 4
>> *
>> * Error: Box line=[ 25.896 13.299 29.595 26.322
>> ]
>>
>> Error: Could not set up '_MMPBSA_complex.mdcrd.0' for
>> reading. Error:
>> Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
>> Error: Error(s) occurred during
>> execution. *
>>
>> Is it an issue in the generation of files for the purpose of my study? or
>> could there be any other issue?
>>
>> The input is :
>> general
>>
>>
>>
>> startframe=240000,endframe=250000,interval=5,verbose=2,keep_files=0,
>> strip_mask=:WAT,28-40
>> /
>>
>> &gb
>> igb=2,saltcon=0.00,surfoff=0.00,surften=0.005,
>> /
>>
>> &pb
>> radiopt=0,inp=1,
>> &nmode
>> nmode_igb=0,drms=0.5,dielc=4,maxcyc=10000
>> /
>>
>> And the command line:
>> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSAall.dat -sp
>> complex.prmtop -cp complexdry.prmtop -rp rec.prmtop -lp ligand.prmtop -y
>> production.nc
>>
>>
>> Regards,
>> Sruthi Sudhakar
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>>
>
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Received on Fri Jan 14 2022 - 23:30:02 PST
