On Mon, 2015-07-27 at 16:16 +0300, Michael Shokhen wrote:
> Dear Amber List members,
>
> I have combined in productive MD distance and torsion restraint in md4.in
> script. The latter calls RST.dist and rst.bb files. The calculation is
> conducted by amber 14 with ff14sb force field in periodic water box.
> Unfortunately the torsion restraint doesn't work. I think there is an error
> in md4.in call of rst.bb file.
> I am a new amber user and I would appreciate your advise how to correct my
> script.
>
>
> Thank you,
> Michael
>
> *md4.in <http://md4.in>*
>
> 30 ns production phase MD
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 1.0,
> cut = 10.0, ntr = 0, iwrap = 1,
> ntc = 2, ntf = 2,
> tempi = 310.0, temp0 = 310.0,
> ntt = 3, gamma_ln = 0.5,
> nstlim = 15000000, dt = 0.002,
> ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
> nmropt=1,
> /
> &wt type='END' /
> DISANG= ../RST.dist
> LISTOUT=POUT
> /
> DISANG1= ../rst.bb
> LISTOUT=POUT
> /
>
>
> *RST.dist*
>
> &rst
> ixpk= 0, nxpk= 0, iat=1030,1692, r1= 1.30, r2= 1.80, r3= 2.80, r4= 3.30,
> rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
> &end
> &rst
> ixpk= 0, nxpk= 0, iat=1030,61, r1= 1.30, r2= 1.80, r3= 3.00, r4= 3.50,
> rk2=50.0, rk3=50.0, ir6=1, ialtd=0,
> &end
>
>
> *rst.bb <http://rst.bb>*
> &rst
> iat=36,51,53,55, r1=0., r2=180., r3=180., r4=360.,
> rk2 = 35., rk3 = 35., /
This is not right. DISANG1 is not a recognized file redirection
keyword, so it is simply ignored. DISANG is where *all* of the
geometric restraint information is read from. So in your example, the
distance restraints are read in, but the torsional restraints are not,
hence the behavior you reported. Get rid of the DISANG1 and second
LISTOUT lines and put the torsional restraint into ../RST.dist instead.
Also, the file redirection cards are not namelists, so you don't need
"/" to signal the end. Simplify your input file to something like the
following:
30 ns production phase MD
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 1.0,
cut = 10.0, ntr = 0, iwrap = 1,
ntc = 2, ntf = 2,
tempi = 310.0, temp0 = 310.0,
ntt = 3, gamma_ln = 0.5,
nstlim = 15000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000, ig = -1,
nmropt=1,
/
&wt type='END' /
DISANG= ../RST.dist
LISTOUT=POUT
And put the torsion restraint into RST.dist.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jul 27 2015 - 07:00:04 PDT
