I think that your sander script (the sander -O etc) needs to say that you
want 2 groups. check page 153 of the Amber9 manual, it describes it there.
On 5/16/07, S. Jamal Rahi <sjrahi.mit.edu> wrote:
>
> Hi,
>
> I am trying out the thermodynamic integration tutorials I have found
> online:
> http://amber.scripps.edu/tutorial/shirts/index.html
> or
> http://dasher.wustl.edu/bio5476/labs/lab-05/c162.html
>
> Sander is giving me the same error in both cases and I am unable to find
> any information about it online:
>
>
> -----------------------------------------------------------------------
> Output file:
> ....
> numgroup must be 2 if icfe is set
>
> *** input error(s)
> -----------------------------------------------------------------------
>
>
> In the case of the second tutorial I am following the exact instructions
> I find online:
> ------------------------------------------------------------------------
> Input file:
> Initial minimization of solvent and solute, 9.0 cut
> &cntrl
> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
> ntpr = 10, ntwx = 0, ntwv = 0, ntwe = 0,
> icfe = 1, clambda = 0, klambda = 1,
>
> ntf = 1, ntb = 1,
> cut = 9.0, nsnb = 10,
>
> ibelly = 0, ntr = 0,
>
> imin = 1, maxcyc = 1000,
> ncyc = 5000,
> ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
>
> nscm = 0,
> t = 0.0, dt = 0.002,
>
> temp0 = 300.0, tempi = 300.0,
> ig = 71277, heat = 0.0,
> ntt = 0,
> tautp = 0.2,
> vlimit = 20.0,
>
> ntc = 1, tol = 0.0005,
>
> &end
> ------------------------------------------------------------------------
>
>
> And I start sander by typing:
>
> sander -O -i amber-crown-minall.in -o minall.out -c crown.crd -p
> crown.top -r crown_min.crd -inf crown_min.info
>
>
> Does anybody have any suggestions as to what is going on? I am not sure
> what the error means.
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 20 2007 - 06:07:07 PDT
