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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Received on Thu Mar 16 2017 - 02:30:02 PDT
