Hi everyone,
    I am a new guy to this APBS application, in my case I want to calculate electrostatic potentials also. but there is some problems with several pdb files of my database. some I could get , but the other I could not, for example for "2GEJ", there is a problem with this. after runing APBS there is always a popup saying "unable to assign parameters for the 151 atoms in selection unassigned-------". Did anyone meet this problem? how to solve this problem? Need you help.
   Thanks so much.
   /Changrong




Date: Tue, 25 Nov 2008 16:17:02 +0200
From: pinarknlk@gmail.com
To: gernotf@chemie.fu-berlin.de
CC: apbs-users@lists.sourceforge.net
Subject: Re: [Apbs-users] atom # is off the mesh (ignoring) ERROR

Thank you for your replies.
I am calculating electrostatic energies individually. But one thing about input files confused me. Should i use directly the input files which pdb2pqr gave me or should i omit second part which has the value of 2.00 for the dielectric value of the solvent (sdie). Because, input files are usually constructed based on the value of 78.4 for dielectric coefficient of the solvent?

pdb2pqr result :

read
    mol pqr 0.pqr
end
elec
    mg-auto
    dime 161 129 161
    cglen 103.0795 98.5847 111.3313
    fglen 80.6350 77.9910 85.4890
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
    write pot dx pot
end
elec
    mg-auto
    dime 161 129 161
    cglen 103.0795 98.5847 111.3313
    fglen 80.6350 77.9910 85.4890
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 2.0000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end

print elecEnergy 2 - 1 end
quit



2008/11/21 Gernot Kieseritzky <gernotf@chemie.fu-berlin.de>
Hi!

> these molecules need to be *perfectly* aligned since you're relying on
> this alignment to cancel self-interaction energies.  Please be sure to
> check that the atoms are in the same locations after alignment.

Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment
is not possible in her case since the subunits will adopt slightly
different conformations in the monomer case compared to the dimer
situation.

So, Pinar, what you should do to compute the association energy for the
protein complex (I guess, this is what you ultimately want to achieve)
is to compute the total electrostatic energy for the dimer ( E(d) ) and
the monomers ( E(m1), E(m2) ) individually and then compute the
difference

E(d) - ( E(m1) + E(m2) )

How to compute the total dielectric energy?

E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x,  homogenious)
      ^^^^^^^^^^^^^^^^^^^^^   ^^^^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^^^^
      use 'coulomb.c' in the  APBS with pdie!=sdie  APBS with pdie=sdie
      APBS distribution with                        and no ions
      eps = pdie

The difference E(x, inh) - E(x,hom) will ensure that the grid artifact
cancels.

To compare with possible experimental values in case of protein-protein
association you will also need to include the non-electrostatic
contribution to the solvation energy and add this to E(x).

Greetings,
Gernot


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٩(͡๏̯͡๏)۶ pinar


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