AMBER Archive (2005)

Subject: RE: AMBER: &dipoles in sander

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jan 21 2005 - 12:26:24 CST

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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