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.
>>> 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 ...
>>>>>
>>>>>
>>>>>
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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 ...
>>>
>>>
>>>> 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 ...
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>>>
>>>> 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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>>>>> 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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>>> 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 ...
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>>>
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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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>>> 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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>>> 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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>>> 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
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Received on Wed Jun 28 2017 - 11:30:07 PDT
