oh ok Ross i forget i start my thread
On Wed, Jun 28, 2017 at 2:21 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Please start your own thread.
>
> Bill
>
> On 6/28/17 11:14 AM, Rana Rehan Khalid wrote:
> > 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.
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> >> Dynamics
> >>> and related ...
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> >>> mailman/listinfo/amber>
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
> >>>>
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> >>> mailman/listinfo/amber>
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> >>> mailman/listinfo/amber>
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> List.
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> >>> and related ...
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> >>> mailman/listinfo/amber>
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >>> List. It is designed to provide a forum for users of the AMBER
> Molecular
> >>> Dynamics and related ...
> >>>>>
> >>>>>
> >>>>>
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> >>> mailman/listinfo/amber>
> >>> lists.ambermd.org
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >>> mailman/listinfo/amber>
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> >>> mailman/listinfo/amber>
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >>> mailman/listinfo/amber>
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
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> >>> mailman/listinfo/amber>
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> >>> mailman/listinfo/amber>
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> >>> 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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> >> 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 ...
> >>>>>
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> List.
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> >> Dynamics
> >>> and related ...
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> >>> mailman/listinfo/amber>
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
> >>> and related ...
> >>>
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> >> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
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> List.
> >>> It is designed to provide a forum for users of the AMBER Molecular
> >> Dynamics
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> >>> 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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> >
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Received on Wed Jun 28 2017 - 11:30:08 PDT
