Nubia, Ross
i do not prepare the file like inpcrd and prmtop for my protein system that
consist of heme first i prepare then then i run sander for these input
files. can sander produces the input files without leap ?? first i have to
produce the input kindly tell me i was thing right if wrong then guide me
sorry i am new on amber station and i read some tutorial
On Wed, Jun 28, 2017 at 1:53 PM, Núbia Prates <nnubiaits.hotmail.com> wrote:
> Yes, I did. But I tried sander before and a had no problems.
>
>
> Nubia
>
>
> ________________________________
> De: Núbia Prates <nnubiaits.hotmail.com>
> Enviado: quarta-feira, 28 de junho de 2017 14:52
> Para: AMBER Mailing List
> Assunto: Re: [AMBER] sander do not write rst and mdcrd files
>
> Yes, I did. But I tried sander before and a had any problems.
>
>
> Nubia
>
>
> ________________________________
> De: Bill Ross <ross.cgl.ucsf.edu>
> Enviado: quarta-feira, 28 de junho de 2017 14:44
> Para: amber.ambermd.org
> Assunto: Re: [AMBER] sander do not write rst and mdcrd files
>
> Did you read the install instructions about amber.sh or amber.csh?
>
> Bill
>
>
> On 6/28/17 10:42 AM, Núbia Prates wrote:
> > I dont see any error messages. Now that I have write permission it
> returns:
> >
> > sander: command not found
> >
> >
> > Nubia
> >
> >
> >
> > ________________________________
> > De: Bill Ross <ross.cgl.ucsf.edu>
> > Enviado: quarta-feira, 28 de junho de 2017 14:27
> > Para: amber.ambermd.org
> > Assunto: Re: [AMBER] sander do not write rst and mdcrd files
> >
> > Are you seeing any error messages? Do you have write permission in the
> > directory the files are supposed to appear in?
> >
> > Bill
> >
> >
> > On 6/28/17 10:19 AM, Núbia Prates wrote:
> >> Hello,
> >>
> >>
> >> I am using the following command to generate some files during
> equilibrate step:
> >>
> >>
> >> sander -O -i equi_10.in -p complex.top -c heat.rst -r equi_10.rst -o
> equi_10.out -x equi_10.mdcrd -ref heat.rst
> >>
> >>
> >> The problem is that sander do not write the "equi_10.rst" and "
> equi_10.mdcrd" files.
> >>
> >> Can you help me with that?
> >>
> >>
> >> Regards
> >>
> >> Nubia
> >> _______________________________________________
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Received on Wed Jun 28 2017 - 11:30:08 PDT
