you mean to say that after running sander i use these command in sader
rather then xleap
HEM = loadmol2 hem.mol2 >>>> HEME coordinate file
CYP = loadmol2 cyp.mol2 >>>> CYS (rename this CYS to CYM) residue to make
coordinate bond with HEME
2j2 = loadpdb CYP2J2.pdb >>>> protein system
set 2j2.460.28 element "Fe"
bond 2j2.460.28 2j2.405.8 >>>> making the bond between HEME and CYS #BOND
CYS-S to HEM-FE
set 2j2.405 connect0 2j2.405.1
set 2j2.405 connect1 2j2.405.9
bond 2j2.404.9 2j2.405.1 #BOND CYS to the protein (new CYP residue)
bond 2j2.405.9 2j2.406.1 #As above
addions 2j2 Na+ 0
solvateoct 2j2 TIP3PBOX 10
saveamberparm 2j2 CYP2J2_FE_box.prmtop CYP2J2_FE_box.inpcrd
On Wed, Jun 28, 2017 at 2:12 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
wrote:
> 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
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > lists.ambermd.org
> > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> > >
> > >
> > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > lists.ambermd.org
> > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> > >
> > >
> > >> lists.ambermd.org
> > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> > List. It is designed to provide a forum for users of the AMBER Molecular
> > Dynamics and related ...
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > lists.ambermd.org
> > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> > >
> > >
> > >> AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > lists.ambermd.org
> > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> > >
> > >
> > >> lists.ambermd.org
> > >> AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> > List. It is designed to provide a forum for users of the AMBER Molecular
> > Dynamics and related ...
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > lists.ambermd.org
> > > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
> > >
> >
> >
> > _______________________________________________
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> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> > mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List.
> > It is designed to provide a forum for users of the AMBER Molecular
> Dynamics
> > and related ...
> >
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jun 28 2017 - 11:30:06 PDT
