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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Received on Thu Mar 16 2017 - 03:00:02 PDT
