OK, this was a good suggestion- it appears as if certain atoms in the trajectory file become distorted as the number of simulation steps increases. I think the problem is with the small-molecule ligand (CTZ) in binding pocket of the protein.
Originally, there were too many bonds to each atom in the CTZ molecule. I used the SMILE software followed by REDS to get the right bond lengths and thus make it so each atom had the proper bond lengths and corrersponding # of Bonds (pdb file attached: (CTZ05.pdb). I then used antechamber to make the param and crd files. I followed the antechamber amber tutorial for this.
The problem now appears to be the complex. The CTZ molecule in the binding pocket has too many bonds to it and this is probably causing the problem (attached pdb 2psj_ctz_compex...pdb). I originally got the complex from a molgro file in the mol2 format.
I can't put the protein/ligand complex through SMILES again.
How can I fix this problem
Thanks,
Chris
________________________________
From: Ross Walker <ross.rosswalker.co.uk>
To: 'Chris Chris' <alpharecept.yahoo.com>; 'AMBER Mailing List' <amber.ambermd.org>
Sent: Tuesday, May 8, 2012 9:42 AM
Subject: Re: [AMBER] help with pmemd .in file
Try setting ntwx=1 and running for about 50 steps or so. Then take a look at
the trajectory and see if anything looks wrong. Your temperature is going up
extremely quickly given you are using the weight restraints and the langevin
thermostat. This suggests there could be something wrong with your initial
structure.
All the best
Ross
> -----Original Message-----
> From: Chris Chris [mailto:alpharecept.yahoo.com]
> Sent: Tuesday, May 08, 2012 9:23 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] help with pmemd .in file
>
> OK,
>
> I did that and it did indeed work (.out file attached), however with
> far fewer MD steps than I would have like to perform (nstlim =10). Is
> it not possible to get all 25,000 in?
>
> Here was the .in file
>
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=10,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=1,
> ntpr=1, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> ntr=1,
> nmropt=1
> /D
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
> write
> 10.0
> RES 1 252
> END
> END
>
>
>
> ________________________________
> From: David A Case <case.biomaps.rutgers.edu>
> To: Chris Chris <alpharecept.yahoo.com>; AMBER Mailing List
> <amber.ambermd.org>
> Sent: Tuesday, May 8, 2012 5:15 AM
> Subject: Re: [AMBER] help with pmemd .in file
>
> On Mon, May 07, 2012, Chris Chris wrote:
> >
> > > Can someone see what I did wrong here?
> > >
> > > heat 2psj ctz first time
> > > &cntrl
> > > imin=0,irest=0,ntx=1,
> > > nstlim=25000,dt=0.002,
> > > ntc=2,ntf=2,
> > > cut=8.0, ntb=1,
> > > ntpr=500, ntwx=500,
> > > ntt=3, gamma_ln=2.0,
> > > tempi=0.0, temp0=300.0,
> > > ntr=1,
> > > nmropt=1
> > > /
>
> ..
>
> <broken_record>
> When you have problems, set nstlim=10 and ntpr=1; doesn't always help,
> but
> certainly narrows down the list of possible problems.
> </broken_record>
>
> ....dac
>
>
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- application/octet-stream attachment: CTZ05.pdb
Received on Tue May 08 2012 - 22:00:03 PDT
