Hi Changqing,
You could try viewing it with xleap. Also try saving a pdb in weblabviewer,
and compare the format to the ambpdb-generated pdb.
Minimization usually does so little that restraints are more trouble
that they're worth. You could measure rms between inpcrd and restrt to
see how much movement there is.
Bill
Changqing Yan <ycqchemical.gmail.com> wrote:
> Hi Bill,
>
> Thanks a lot for your reply. I use ambpdb script to generate the pdb
> structure, and view it in weblabviewer. Is there a problem?
>
> Is there any problem with my minimization input ?
>
> Initial minimisation of protein side chains and ions
> &cntrl
> imin=1, maxcyc=4000,ncyc=2000,
> cut=12, ntb=0, igb=1, ntr=1,
> /
> Hold Res 1-1466 protein backbone constrained
> 10.0
> FIND
> CA * * *
> SEARCH
> RES 1 1466
> END
> Go on
> 10.0
> FIND
> C * * *
> SEARCH
> RES 1 1466
> END
> Go on
> 10.0
> FIND
> N * * *
> SEARCH
> RES 1 1466
> END
> END
>
> Rgds,
> C.Q.
>
> ------------------
> Message: 6
> Date: Wed, 20 Feb 2013 19:36:17 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Amber 11 Installment problem
> To: amber.ambermd.org
> Message-ID: <n6ye6f83h3mjoyph7i0xuih3.1361417777579.email.android.com>
> Content-Type: text/plain; charset=utf-8
>
> How did you generate the pdb, and what program did you view it in?
>
> One possibility is that there is a format incompatibility.
>
> Bill
>
> -------- Original message --------
> From: Changqing Yan <ycqchemical.gmail.com>
> Date:
> To: amber.ambermd.org
> Subject: [AMBER] Amber 11 Installment problem
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Received on Sat Feb 23 2013 - 12:00:03 PST
