[MMTK] PDB producing, amber_atom_charges

Konstantinos Makrodimitris kmakr7 at msn.com
Thu Jun 5 21:31:30 EDT 2003


Hi,
I'd like to be more specific after your answer please.

>From: Konrad Hinsen <hinsen at cnrs-orleans.fr>
>To: "Konstantinos Makrodimitris" <kmakr7 at msn.com>, mmtk at python.net
>Subject: Re: [MMTK] PDB producing, amber_atom_charges
>Date: Mon, 2 Jun 2003 23:59:04 +0200
>
>
> > I'd like to ask your advice for producing easy and not by hand PDBs for
> > aminoacids,
> > proteins, peptides with protected groups in a way to be consistent to
> > PDB naming conventions for atoms in proteins and to MMTK utility of 
>course.
>
>From what kind of input information would you like to create such PDB 
>files?


I am interested in 2 cases:

a) I could find in scientific websites files with no default PDB format for 
biomolecules eg
ALANINE
-----------
ATOM      1  N   ALA  0001      -1.053   1.300   0.614
ATOM      2  CA  ALA  0001      -0.304   0.032   0.746
ATOM      3  C   ALA  0001       0.770  -0.014  -0.311
ATOM      4  O   ALA  0001       1.952  -0.167  -0.047
ATOM      5  H   ALA  0001      -1.805   1.385   1.386
ATOM      6  O   ALA  0001       0.354   0.125  -1.567
ATOM      7  H   ALA  0001      -1.522   1.368  -0.358
ATOM      8  H   ALA  0001       0.176   0.013   1.740
ATOM      9  C   ALA  0001      -1.237  -1.200   0.610
ATOM     10  H   ALA  0001      -2.007  -1.183   1.397
ATOM     11  H   ALA  0001      -0.655  -2.129   0.709
ATOM     12  H   ALA  0001      -1.737  -1.199  -0.371
ATOM     13  H   ALA  0001       1.100   0.082  -2.154
CONECT    1    2    5    7
CONECT    2    1    3    8    9
CONECT    3    2    4    4    6
CONECT    4    3    3
CONECT    5    1
CONECT    6    3   13
CONECT    7    1
CONECT    8    2
CONECT    9    2   10   11   12
CONECT   10    9
CONECT   11    9
CONECT   12    9
CONECT   13    6


Is there a way for example using MMTK.PDB module to create a residue(or a 
peptide for
more complex case than this) with such format without to change mannually 
H-->1H, C-->CB etc.
If there is such a way then after transformation I could assign AMBER 
partial charges for
such a biomolecule which it could be consisted sometimes with many residues 
of course.

b) In the case that I'd like to simulate a more complex organic molecule in 
MMTK or to
model it in order to use it for a protected group for a peptide.
I could find coordinates in the similar non-default PDB format:
NITROANILIDE
ATOM      1  O           0       2.235   1.226  -0.001  0.00  0.00
ATOM      2  N           0       1.527  -0.000  -0.000  0.00  0.00
ATOM      3  O           0       2.235  -1.226   0.001  0.00  0.00
ATOM      4  C           0       0.130   0.000  -0.001  0.00  0.00
ATOM      5  C           0      -0.566  -1.202  -0.000  0.00  0.00
ATOM      6  C           0      -1.947  -1.198   0.000  0.00  0.00
ATOM      7  C           0      -2.637   0.000  -0.001  0.00  0.00
ATOM      8  C           0      -1.947   1.198  -0.001  0.00  0.00
ATOM      9  C           0      -0.566   1.202   0.004  0.00  0.00
ATOM     10  H           0       3.176   1.005  -0.001  0.00  0.00
ATOM     11  H           0       3.176  -1.005   0.001  0.00  0.00
ATOM     12  H           0      -0.028  -2.138   0.000  0.00  0.00
ATOM     13  H           0      -2.489  -2.133   0.000  0.00  0.00
ATOM     14  H           0      -3.717   0.000  -0.001  0.00  0.00
ATOM     15  H           0      -2.489   2.133  -0.002  0.00  0.00
ATOM     16  H           0      -0.028   2.138   0.004  0.00  0.00
CONECT    1    2   10    0    0
CONECT    2    1    3    4    0
CONECT    3    2   11    0    0
CONECT    4    2    9    5    0
CONECT    5    4    6   12    0
CONECT    6    5    7   13    0
CONECT    7    6    8   14    0
CONECT    8    7    9   15    0
CONECT    9    8    4   16    0

There are 2 subquestions here:
a) How as in the 1) question to assign partial charges and then fit 
(neutral) them with MMTK
in order to make with AMBER94 a coarse representation of the organic 
molecule?
In MMTK database you have only 'water' molecule explicitly defined
and in groups some simple N,C-terminal org.compounds for proteins but
is there a more broad option for more complex?
b)In an earlier email asking about AMBER94 charges you replied that for 
custom cases
the best is to fit the partial charges to an electrostatic potential
surface obtained by quantum chemistry.
Could you be more specific in the quantum utility that does that consistent
with MMTK-AMBER94? Is there a package, website do you suggest?
And in more details which is the procedure in MMTK for partial charge 
calculation
before fitting the charges please?

Best,
Kon

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