> 1) Few amino acids cleaved and detached from the main chain (469 amino acids ), after minimization of the complex.
Is there by any chance a 'TER' line in the pdb at the point of cleavage?
> 2) After equilibration stage, the drug (C16H28N2O4) is considerably moved out ,compared to the X-ray crystallographic structure available in PDB.
You could try some weak distance restraints to hold the drug in place during the initial constant pressure equilibration, perhaps also the warming if the drug starts to move out then.
Bill
On 11/24/15 3:28 AM, Vahid Kshani wrote:
> Dear all
>
> We have started a protein-drug MD simulation, we found the following issues;
>
> 1) Few amino acids cleaved and detached from the main chain (469 amino acids ), after minimization of the complex.
>
> 2) After equilibration stage, the drug (C16H28N2O4) is considerably moved out ,compared to the X-ray crystallographic structure available in PDB.
>
> We will be thankful to you if you recommend suggestions to troubleshoot the issues.
>
> Inputs are mentioned below for your perusal
> Minimization: Minimization to relax initial bad contacts, explicit solvent
> &cntrl
> imin=1,
> ncyc=1000,
> maxcyc=5000,
> ntpr=50,
> cut=8,
> restraintmask='!:WAT&.CA,C,O,N'
> restraint_wt=10.0,
> /
> Heat
> Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=10.0, VALUE2=300.0,
> /
> &wt TYPE='END' /
>
> Equilibration
> Explicit solvent molecular dynamics constant pressure MD
> &cntrl
> imin=0, irest=1, ntx=5,
> ntpr=1000, ntwx=1000, nstlim=2000000,
> dt=0.002, ntt=3, tempi=300,
> temp0=300, gamma_ln=1.0, ig=-1,
> ntp=1, ntc=2, ntf=2, cut=8,
> ntb=2, iwrap=1, ioutfm=1,
> /
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Received on Tue Nov 24 2015 - 04:00:04 PST
