I figured it out.
The problem was that I was using pmemd setup and running it using sander. I understood the problem when I run it using pmemd.cuda, which directed me to use pmemd instead as CUDA doesn't support TI method.
________________________________________
From: Bill Ross [ross.cgl.ucsf.edu]
Sent: Thursday, March 16, 2017 10:36 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Issues running TI simulations
Hi Sowmya,
I don't know what it is, it may be valid, it's just different. Perhaps a
left-over comment.
Bill
On 3/16/17 2:30 AM, Sowmya Indrakumar wrote:
> Hi Bill,
> Thanks for your suggestions.
>
> There is no other error message that I get.
> I will debug the way you have suggested.
> I am not very sure about the importance of having this (see below)
>
> * !method 2:
> !scmask1 = '', scmask2 = '',*
>
> as I am leaving it blank anyways. I would like to know more about having this.
>
> Thanks
> Regards
> Sowmya
>
>
> ________________________________________
> From: Bill Ross [ross.cgl.ucsf.edu]
> Sent: Thursday, March 16, 2017 10:24 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Issues running TI simulations
>
> Is there no other error output, e.g. about what field or line the error
> is on?
>
> If not, you can try deleting one thing at a time and retrying. I would
> start with the ! lines.
>
> Bill
>
>
> On 3/16/17 2:10 AM, Sowmya Indrakumar wrote:
>> Dear All,
>> I am trying to minimize my system with these parameters :
>>
>> Here is the input file:
>>
>> minimisation
>> &cntrl
>> imin = 1, ntmin = 2, maxcyc = 1000,
>> ntpr = 20, ntwe = 20,
>> dx0 = 1.0D-7,
>> ntb = 1,
>> iwrap = 1,
>> icfe = 1, ifsc = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
>> logdvdl = 0,
>> timask1 = '.37,38,39,40,41,42,43,44,45,46,420,421,422,423,424,425,426,427,428,429',
>> timask2 = '.576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597',
>> scmask1 = '.37,38,39,40,41,42,43,44,45,46,420,421,422,423,424,425,426,427,428,429',
>> scmask2 = '.576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597',
>>
>> !method 2:
>> !scmask1 = '', scmask2 = '',
>> /
>>
>> &ewald
>> /
>>
>>
>> I get this error message in the output file:
>>
>> error in reading namelist cntrl
>>
>> I have made sure &ewald and &cntrl is in the second column.
>> Is there anything wrong that I am doing. I look forward for your suggestions.
>>
>> Thanks
>> Regards
>> Sowmya
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ________________________________________
>> From: Hai Nguyen [nhai.qn.gmail.com]
>> Sent: Wednesday, March 15, 2017 2:11 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] How to get parmed.py script?
>>
>> Hi
>>
>> parmed.py is renamed to parmed (no .py)
>>
>> parmed protein.parm7 ...
>>
>> Hai
>>
>> On Wed, Mar 15, 2017 at 5:31 AM Sowmya Indrakumar <soemya.kemi.dtu.dk>
>> wrote:
>>
>>> Dear All,
>>> With the IT support in my department, I tried to get the parmed.py script.
>>> But failed in doing the same.
>>> Compiling the latest version of parmed from the github source just
>>> createsthe parmed and xparmed executable files and not the *.py files.
>>>
>>> For instance, this is what I wish to do using parmed.py
>>>
>>> python $AMBERHOME/bin/parmed.py protein.parm7 <<_EOF
>>> loadRestrt protein.rst7
>>> setOverwrite True
>>> tiMerge :1-40 :41-80 :4,44 :30,70
>>> outparm merged_protein.parm7 merged_protein.rst7
>>> quit _EOF
>>>
>>>
>>> I need your inputs in this regard.
>>>
>>> Thanks in advance
>>> Regards
>>> Sowmya
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
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>>
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>> AMBER mailing list
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Received on Thu Mar 16 2017 - 05:30:04 PDT
