[AMBER] Issues running TI simulations

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Thu, 16 Mar 2017 09:10:04 +0000

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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 16 2017 - 02:30:02 PDT
Custom Search