AMBER Archive (2005)

Subject: RE: AMBER: &dipoles in sander

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sat Jan 22 2005 - 03:47:50 CST

Hi Ross and other amber folks,

I guess I have forgotten to indicate before
that my molecule is a small single unit (MW~300 Da).
Isn't it just possible to define two (or one?)
amino center(s) within the same unit using
the &dipoles option?

I have tried the following input2 , but I
received a similar error message in output2.

input2:

 &cntrl
imin=0, nstlim=1, cut=8, ntb=1,
ntpr=1,
ipol=1,
 &end
 &dipoles
GROUP1 1-1 MOL->MOL
ATOM 22 12 # 22 12 are positively charged Ns
END
 &end

output2:

NSTEP = 0 TIME(PS) = 0.000
TEMP(K) = 0.00 PRESS = 0.0
Etot = -7265.1113 EKtot = 0.0000
EPtot = -7265.1113 BOND = 386.6703
ANGLE = 9.4645 DIHED = 26.3319
1-4 NB = 9.2914 1-4 EEL = 75.2922
VDWAALS = 1050.2376 EELEC = -8818.8029
EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -3.5963 E3BODY = 0.0000
Dipole convergence: rms = 0.497E-04
temperature = 0.00

-----------------------------------------------------------
-------------------

 ------------------------------- DIPOLE INFO
---------------
-------------------

 NSTEP = 0 TIME(PS) = 0.000

     rfree: End of file on unit 5

If the &dipoles option is not designed to give
dipole info (i.e.; inducable dipole) for
intra-residual atomic groups, would it still be
likely to utilize the EPOLZ info above to compare
polarizabilities between different conformers of
the same molecule?

regards,

Jenk

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Dear Jenk,
>
> > this time adding &dipoles option in my input file
> for
> > a charged amino group as follows,
> >
> > input2 :
> >
> > &cntrl
> > imin=1, maxcyc=1,
> > ntpr=1,
> > ntr=1,
> > ipol=1,
> > /
> > &dipoles
> > NEA.1.N6
> > &end
> > Group input for restrained atoms
> > 100.0
> > RES 1
> > END
> > END
>
> The problem here concerns the way I implemented the
> &dipoles option. When I
> put it into sander originally it was just for
> internal testing purposes.
> Later, however, we realised it might be a useful
> option. Unfortunately the
> printing of the dipoles involves the use of group
> definitions for the
> molecules to be printed. These groups are not unique
> and so it will not work
> if you use group definitions for other things, such
> as in your case
> restraints. I know this is a pain but at the time it
> was the quickest way to
> implement it. Hence in order to be able to print the
> dipole info you will
> need to turn the restraints. It may be possible to
> use NMR restraints
> instead of the harmonic restraints as this should
> work alongside the dipole
> printing.
>
> If you just want the permanent dipole as a function
> of time then in theory
> you can post process an mdcrd file to get this
> information. Ptraj may
> support this but I'd have to check. As for the
> inducible dipoles there is
> currently no way to obtain this data other than
> using the &dipoles option.
> It would fairly easy to modify the code to write the
> indcible dipole info
> for "every" residue but much more involved to allow
> groups to be selected
> independently of the restraint groups.
>
> Here is an example input for crambin:
>
> &cntrl
> imin=0,ntpr=1, ntwx=0, ntwr=0,
> ntx=7, irest=1,
> cut=12.0, vlimit=10,
> dt=0.001, nstlim=10,
> ntb=2, ntt=1, tempi=300.0, temp0=300.0,
> tautp=0.5,
> ntp=1, pres0=1.0, taup=2.0,
> ntf=1, ntc=1,
> ntxo=1,ioutfm=0,
> ipol=1
> &end
> &dipoles
> GROUP1 1-2 NTHR->THR
> ATOM 15 18
> END
> GROUP2 11-12 SER->ASN
> ATOM 154 157
> END
> GROUP3 31-32 GLY->CYX
> ATOM 440 443
> END
> GROUP4 41-42 PRO->GLY
> ATOM 576 579
> END
> END
> &end
>
> And an example of the output:
>
> NSTEP = 1 TIME(PS) = 20.001 TEMP(K) =
> 298.79 PRESS = -832.9
> Etot = -33111.0869 EKtot = 11124.7005
> EPtot = -44235.7874
> BOND = 6328.1537 ANGLE = 363.9958
> DIHED = 456.9249
> 1-4 NB = 164.8543 1-4 EEL = 2564.8952
> VDWAALS = 9676.3547
> EELEC = -63613.4129 EHBOND = 0.0000
> RESTRAINT = 0.0000
> EKCMT = 4154.5316 VIRIAL = 6710.6480
> VOLUME = 142134.4198
> EPOLZ = -177.5531 E3BODY = 0.0000
> Dipole convergence: rms = 0.402E-04 temperature =
> 0.00
>
> Density = 0.8867
>
>
----------------------------------------------------------------------------
> --
>
> ------------------------------- DIPOLE INFO
> ----------------------------------
>
> NSTEP = 1 TIME(PS) = 20.001
> x y
> z Total
> DIPGRP - 1: centre of mass : 35.760 30.349
> 26.771
> DIPGRP - 1: permanent dipole : 1.515 -1.094
> -4.035 4.446 D
> DIPGRP - 1: induced dipole : -0.046 -0.182
> -0.067 0.199 D
> DIPGRP - 1: total dipole : 1.469 -1.276
> -4.102 4.540 D
> x y
> z Total
> DIPGRP - 2: centre of mass : 22.580 24.596
> 23.542
> DIPGRP - 2: permanent dipole : 0.602 -2.987
> 3.153 4.385 D
> DIPGRP - 2: induced dipole : 0.062 -0.255
> 0.063 0.269 D
> DIPGRP - 2: total dipole : 0.663 -3.242
> 3.216 4.614 D
> x y
> z Total
> DIPGRP - 3: centre of mass : 27.023 29.071
> 33.086
> DIPGRP - 3: permanent dipole : -3.934 0.437
> -1.955 4.414 D
> DIPGRP - 3: induced dipole : -0.156 0.206
> -0.050 0.263 D
> DIPGRP - 3: total dipole : -4.090 0.643
> -2.005 4.600 D
> x y
> z Total
> DIPGRP - 4: centre of mass : 37.013 23.185
> 34.968
> DIPGRP - 4: permanent dipole : 3.209 0.948
> 2.770 4.344 D
> DIPGRP - 4: induced dipole : 0.380 -0.095
> 0.146 0.418 D
> DIPGRP - 4: total dipole : 3.589 0.852
> 2.916 4.702 D
> ----------------------------- END DIPOLE INFO
> --------------------------------
>
> I hope this helps,
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available
> on request |
>
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