Dear Prof. Case,
Thank you for your email,
Please allow me to interpret your suggestion one by one as I am not so good
in Amber.
1. What you need are one frame (doens't matter from what part of the
simlation), and get the prmtop files for the receptor, ligand and complex.
Ans: I think I prepare make prmtop files from trajectory file with the
following command:
ante-MMPBSA.py -p complex.prmtop -c com.prmtop -s '!:1-1079' -r
receptor.prmtop -m :1-1078 -l ligand.prmtop
please correct if I am wrong . In my system: receptor+ligand=1079 residues
2. Look at all three structure visually to make sure they are what you
want.
Ans: Really, I don't have any idea how to visualize prmtop files.
Yesterday, I make pdb file using cpptraj command with input prmtop and rst
file for certain time of simulation, and it can be visualized well.
3. Run a single step minimization (single-point energy
calculation) on all three,
Asn: So I will do minimization step again, and the prmtop files is from
answer number 2 and crd file is the same as I used in the previous
minimization.
4. and try to figure out why the sum of the ligand + receptor bond energy
is not the same as the complex bond
energy.
Ans: Here really I do not have idea also.
5. You may need to create a much smaller system (e.g. just a part of the
receptor) to try to figure this out.
Ans: I will cut some part of my system, so the final file would have less
than 1079 residues.
Please give me any suggestion.
Thank you.
Nadaafiva
Pada tanggal Sen, 13 Apr 2020 pukul 19.04 David A Case <
david.case.rutgers.edu> menulis:
> On Mon, Apr 13, 2020, Nada Afiva wrote:
>
> >Based on your suggestion, I extracted the pdb files after striping water
> >and ion molecules in each step of MD as I previously performed, they are
> >minimization1.pdb,
> >minimization2.pdb, minimization3.pdb, heating1.pdb, heating2.pdb,
> >heating3.pdb, equilibration1, equlibration2, equilibration3,
> >production1, production at 20 ns, and production at 40 ns.
>
> What you need are one frame (doens't matter from what part of the
> simlation), and get the prmtop files for the receptor, ligand and
> complex. Look at all three structure visually to make sure they are
> what you want. Run a single step minimization (single-point energy
> calculation) on all three, and try to figure out why the sum of the
> ligand + receptor bond energy is not the same as the complex bond
> energy.
>
> You may need to create a much smaller system (e.g. just a part of the
> receptor) to try to figure this out.
>
> ...good luck...dac
>
>
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Received on Mon Apr 13 2020 - 19:00:02 PDT
