AMBER Archive (2003)

Subject: Polarization simulation

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Thu Mar 20 2003 - 03:55:33 CST

Dear AMBER community,
I'd like to ask about polarization simulation; having the following input
(at the bottom of the mail) , I get this error:
> namelist read: variable not in namelist
> apparent state: unit 5 named MINH.in
> last format: list io
> lately reading sequential formatted external IO
> Abort (core dumped)

Is my input wrong? I read in the manual that polarizable simulations run
with ew_type =1 or 2, but option 2 is not in the manual!
How shall one treat frc_int parameter?

Is there something special about compilation of sander for polarizable
simulations?

Thanks for your advice.

All the best,

  Martin Lepsik

> const.V, no SHAKE, belly minimization of hydrogens
> &cntrl
> imin = 1, maxcyc = 1000,
> ncyc = 250, drms=0.1,
> ntpr = 10, ntwx=250,
> cut = 10.0, nsnb = 10,
> ntr = 0, ibelly=1,
> ipol = 1, indmeth = 1,
> &end
> Move Hydrogens
> FIND
> * H * *
> * HC * *
> * H1 * *
> * HA * *
> * HO * *
> * HS * *
> * HW * *
> * HP * *
> * H4 * *
> * H5 * *
> SEARCH
> RES 1 12020
> END
> Move inhibitor Hydrogens
> FIND
> * hn * *
> * hc * *
> * h1 * *
> * ha * *
> * ho * *
> * hs * *
> * hw * *
> * hp * *
> * h4 * *
> * h5 * *
> SEARCH
> RES 1 12020
> END
> END
> -------------------------------------------------------------------------- 

--
> ----
> Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
> +420/2/20183-292
> Dept. of Theor Chem & Center for Complex molecular Systems and
Biomolecules
> Institute of Organic Chemistry and Biochemistry (IOCB)
> Flemingovo nam 2,
> Czech Academy of Sciences,
> 166 10, Prague 6,
> Czech Rep.
> URL: www.uochb.cas.cz/~teochem