thanks for your help, i checked the atom number and found sth wrong.thank you!
-linda
> -----Original E-mail-----
> From: "Sushil Mishra" <sushilbioinfo.gmail.com>
> Sent Time: 2010-6-23 14:48:44
> To: "AMBER Mailing List" <amber.ambermd.org>
> Cc:
> Subject: Re: [AMBER] about alanine scanning
>
> Please check in input file properly, that u have given correct atom number
> in MARKED as well as ALASCAN section. or u can write the short detail with
> mm_pbsa.in to us.
>
> ..Sushil
>
> On Wed, Jun 23, 2010 at 6:25 AM, <lidansa.mail.ustc.edu.cn> wrote:
>
> > Amber10
> >
> >
> > > -----Original E-mail-----
> > > From: "Sushil Mishra" <sushilbioinfo.gmail.com>
> > > Sent Time: 2010-6-23 0:42:24
> > > To: "AMBER Mailing List" <amber.ambermd.org>
> > > Cc:
> > > Subject: Re: [AMBER] about alanine scanning
> > >
> > > which version of AMBER are u using ??
> > >
> > >
> > > On Tue, Jun 22, 2010 at 5:47 PM, <lidansa.mail.ustc.edu.cn> wrote:
> > >
> > > > Dear all:
> > > > I use mm_pbsa.pl to perform alanine scaning, and I mutated two
> > > > residues to ala. but received the error in alanine_scanning.log below.
> > Is
> > > > there anyone who has dealt with this issue before? thank you for your
> > help!
> > > > =>> Checking sanity
> > > > Checking GENERAL
> > > > Implicit SAS calc by sander
> > > > Checking GC
> > > > Checking AS
> > > > Checking TRAJ
> > > > Checking MM
> > > > Checking PB
> > > > Checking GB
> > > >
> > > > =>> Creating input
> > > > Sander input
> > > > PBSA input
> > > > make_crd input
> > > >
> > > > =>> Creating coordinates
> > > > Executing makecrd
> > > >
> > > > Amber8 Module: make_crg_hg
> > > >
> > > > usage: make_crd_hg < trajectory_file
> > > >
> > > > Box info found: 73.8120000000000 73.8120000000000
> > > > 73.8120000000000
> > > > Something wrong with NGR 3139 3149
> > > >
> > > >
> > > > linda
> > > >
> > > >
> > > >
> > > >
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Received on Wed Jun 23 2010 - 02:00:03 PDT
