Aha - you do not run sander from xleap, it needs to be run separately.
tleap is easier if you don't need graphics, since you can copy - copy is
broken in xleap, but you can find the history in leap.log.
Bill
On 6/28/17 11:04 AM, Rana Rehan Khalid wrote:
> this is the error sir how i copy the command from xleap because when i
> select the command and ctrl-c it does not copy here is the image i send you
>
> On Wed, Jun 28, 2017 at 1:55 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> 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
>>>>> _______________________________________________
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Received on Wed Jun 28 2017 - 11:30:04 PDT
