Thank you Shailesh! It worked.
Nubia
________________________________
De: SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
Enviado: quarta-feira, 28 de junho de 2017 15:12
Para: AMBER Mailing List
Assunto: Re: [AMBER] sander do not write rst and mdcrd files
Hi,
May be you can source amber.sh or amber.csh in your . bashrc or . cshrc
file to avoid setting AMBERHOME environment variable every time
On Jun 28, 2017 8:06 PM, "Núbia Prates" <nnubiaits.hotmail.com> wrote:
> Bill,
>
>
> Yes I was, then I figure that I have to set AMBERHOME environment variable
> always a new terminal is open. Besides, with the write permissions I can
> see the files generated by sander.
>
>
> Thank you!!!
>
>
> Núbia
>
>
> ________________________________
> De: Bill Ross <ross.cgl.ucsf.edu>
> Enviado: quarta-feira, 28 de junho de 2017 14:55
> Para: amber.ambermd.org
> Assunto: Re: [AMBER] sander do not write rst and mdcrd files
>
> Are you running any differently? Perhaps you need to source amber.sh in
> your run script?
>
> If this doesn't help, please copy/paste all commands you are using (and
> script contents if any).
>
> Bill
>
>
> On 6/28/17 10:52 AM, Núbia Prates wrote:
> > 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
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jun 28 2017 - 11:30:09 PDT
