Running system for CYP450 which contain HEME prosthetic group [NAMD] and some questions.

[KyoungPyo Kwon]

Hellow all of my respective seniors.
I'm undergraduate student in Korea.
Nowadays I try to run gmx_MMPBSA using CYP450 protein + ligand. but i faced some problem like below figure.
My system can't skip cleaning session during 10 hours. So anyone give to me some advises about that ?

and if u possible i want to recieve some answer like
1. For the per residue amino acid energy calculation which program can i used ?
2. Is there any instruction about prosthetic group gmx_MMPBSA calculation using NAMD?  

I really appriciate ur kindly attention thank u :)

[marioe911116]

Hi there! 

1-the issue with "cleaning trajectories" has been solved... please check this issue (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/213)

2- for per-residue you can check this tutorial (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/examples/Decomposition_analysis/)

have a go and let us know how it goes... 

[KyoungPyo Kwon]

Hello! Thank u for ur kindly answer.

I solved 1st issue, but i found some problem for make pdb and top file from psf and pdb file.
During gmx_MMPBSA, trajectory file and pdb, top show meassage like  Doesn't match atom [6079] [6020].
I can show message like attached figure.

How can i solve this problem ?

For the converting of pdb and top file i used same parameter in NAMD simulation.

2022년 4월 11일 월요일 오후 3시 27분 34초 UTC+9에 marioe911116님이 작성:

[marioe911116]

could you send around the files you are using? is not clear in the error message what's going wrong

[KyoungPyo Kwon]

 I sent the data through a personal message. Please tell me if you haven't received an email related to this.

Thank u :) !!

2022년 4월 11일 월요일 오후 6시 1분 59초 UTC+9에 marioe911116님이 작성:

[KyoungPyo Kwon]

I used NAMD for molecular dynamics simulation. So all file format need to convert GMX.

And my protein has prosthetic group as HEME which contain FE atom.

Hello, I solved this problem according to the advice of the person who wrote the answer.

My problem is "The number of atoms was mismatched between trajectory[6079]  and pdb,psf[6020] files."

This error is believed to have occurred due to the disappearance of some information when using the PARMED.

So some code was fixed like below

    

Trajectory converting

    >trajin NPT_production.dcd
    >strip :POT,CLA,TIP3,SOD
    >trajout traj.xtc

    >trajout ionized_1.pdb onlyframes 1
    >run
    >exit

Gromacs file building

psf = pmd.load_file('ionized.psf')
psf.strip(':POT, CLA, TIP3, LIT, SOD, RUB, CES, BAR')
psf.coordinates = pmd.load_file('ionized_1.pdb').coordinates # note that I do the strip first and then load the coordinates, otherwise ends up in a mismatch error
params = pmd.charmm.CharmmParameterSet('parm/par_all36_prot.prm',
                                       'parm/par_all36_na.prm',
                                       'parm/par_all36_lipid.prm',
                                       'parm/par_all36_carb.prm',
                                       'parm/par_all36_cgenff.prm',
                                       'parm/toppar_water_ions_namd.str',
                                       'parm/lig.prm' ,
                                       'parm/toppar_all36_prot_heme.str')
psf.load_parameters(params)
psf.save('gromacs_1.top')
psf.save('gromacs_1.pdb')

After change like this my system was working !

I really appreciate kindly advice :)

2022년 4월 12일 화요일 오전 12시 58분 29초 UTC+9에 KyoungPyo Kwon님이 작성: