Dear Amber development Group
Our lab purchased Amber2020 recenetly which is a wonderful software package in the area MD simulated ,we simulated a enzyme using QM/MM by amber20 , a prmtop and inpcrd of enzyme substrate and protein complex file were generated successfully, but there was something error occured when we generated new prmtop and inpcrd file from the result which come from a equil mdcrd snap by a MM simulating, the detail step as follows:
tleap -f oldff/leaprc.ff99SB
> source leaprc.gaff
> loadamberparams MFA.frcmod (ligand)
> loadoff MFA.lib (ligand)
> source leaprc.water.tip3p
> mol = loadpdb DLP-499-cut-wat.pdb (same residue as (all within 5 of protein), $ set QM [atomselect top "same residue as (all within 5 of protein)"] , $QM writepdb DLP-499-cut-wat.pdb) )
> charge mol
> addions mol Na+ 0
> saveamberparm mol DLP-499-cut-wat.prmtop DLP-499-cut-wat.inpcrd
> quit
the error information is as follows when we run "mol = loadpdb DLP-499-cut-wat.pdb" :
Warning: -no luck
Creating new UNIT for residue: MFA sequence: 1
Created a new atom named: C1 within residue: .R<MFA 1>
Created a new atom named: O1 within residue: .R<MFA 1>
Created a new atom named: C2 within residue: .R<MFA 1>
Created a new atom named: C3 within residue: .R<MFA 1>
Created a new atom named: C4 within residue: .R<MFA 1>
Created a new atom named: C5 within residue: .R<MFA 1>
Created a new atom named: C6 within residue: .R<MFA 1>
Created a new atom named: C7 within residue: .R<MFA 1>
Created a new atom named: C8 within residue: .R<MFA 1>
Created a new atom named: C9 within residue: .R<MFA 1>
Created a new atom named: C10 within residue: .R<MFA 1>
Created a new atom named: O2 within residue: .R<MFA 1>
Created a new atom named: O3 within residue: .R<MFA 1>
Created a new atom named: C11 within residue: .R<MFA 1>
Created a new atom named: O4 within residue: .R<MFA 1>
Created a new atom named: H1 within residue: .R<MFA 1>
Created a new atom named: H2 within residue: .R<MFA 1>
Created a new atom named: H3 within residue: .R<MFA 1>
Created a new atom named: H4 within residue: .R<MFA 1>
Created a new atom named: H5 within residue: .R<MFA 1>
Created a new atom named: H6 within residue: .R<MFA 1>
Created a new atom named: H7 within residue: .R<MFA 1>
Created a new atom named: H8 within residue: .R<MFA 1>
Created a new atom named: H9 within residue: .R<MFA 1>
Created a new atom named: H10 within residue: .R<MFA 1>
Created a new atom named: H11 within residue: .R<MFA 1>
Created a new atom named: H12 within residue: .R<MFA 1>
Created a new atom named: OXT within residue: .R<VAL 339>
we wonder why generated prmtop and inpcrd of complex file without water were successfully, but failure upon deletion of all water molecules beyond a shell of 5 around enzyme-substrate complex.
we will much appreciate for any suggestion for the solution in advance.
College of Food science and technology
Nanjing Agricultural University
Zhihong XIn
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Received on Tue Jul 07 2020 - 08:00:03 PDT
