Hi,
we are preparing our compounds in Avogadro 1.1.1.1 and then
use them in Gromacs and NAMD. We save the compounds as mol2 file in
Avogadro, than we import the mol2 file to some parametrization program
such as AcPype. AcPype will give you a PDF format for the ligand that
you can stick at the end of your PDB file with protein coordinates.
The PDB can be tan converted to gmx with pdb2gmx or to psf with VMD
psf builder. Hope this helps, it works for us great in the last two
years
Cheers,
www.svedruziclab.com
On 2017-04-23 10:12, Nash,
Anthony wrote:
> Hi all,
>
> I am trying to recreate the unit cell
assemblage of 4z1r (visible using the PDB NGL viewer on the website).
>
> After importing my structure and checking the unit cell dimensions, I
set the space group (5 c 2y c 1 2 1 as determined using Maestro) then
select "Fill Unit Cell". Visually, everything looks good. But
unfortunately, all means of identifying the atom and the corresponding
residue is lost in the exported pdb and matching/replicated atoms as
listed together rather than in their corresponding residue order. I plan
on importing this into Gromacs, but in its current state the .pdb file
is impossible to read.
>
> E.g.,
>
> HETATM 1 N UNL 1 3.631 3.685
8.676 1.00 0.00 N
>
> HETATM 2 N UNL 2 165.943 3.685 16.225 1.00 0.00
N
>
> HETATM 3 N UNL 3 89.418 10.655 8.676 1.00 0.00 N
>
> HETATM 4
N UNL 4 80.156 10.655 16.225 1.00 0.00 N
>
> HETATM 5 C UNL 5 4.854
4.502 8.763 1.00 0.00 C
>
> HETATM 6 C UNL 6 164.720 4.502 16.138 1.00
0.00 C
>
> HETATM 7 C UNL 7 90.640 11.472 8.763 1.00 0.00 C
>
>
HETATM 8 C UNL 8 78.933 11.472 16.138 1.00 0.00 C
>
> HETATM 9 C UNL 9
6.049 3.864 8.047 1.00 0.00 C
>
> HETATM 10 C UNL 10 163.525 3.864
16.854 1.00 0.00 C
>
> HETATM 11 C UNL 11 91.836 10.833 8.047 1.00
0.00 C
>
> HETATM 12 C UNL 12 77.738 10.833 16.854 1.00 0.00 C
>
>
HETATM 13 O HOH 13 5.956 2.719 7.616 1.00 0.00 O
>
> HETATM 14 O HOH
14 163.618 2.719 17.285 1.00 0.00 O
>
> HETATM 15 O HOH 15 91.743
9.688 7.616 1.00 0.00 O
>
> HETATM 16 O HOH 16 77.831 9.688 17.285
1.00 0.00 O
>
> Any idea how to fix this?
>
> I'm beginning to think
the only way around this would be to import my asymmetric unit structure
into Gromacs, replicate the protein, identify the x,y,z location of a
central atom from within Avogadro of one of the three replicated
molecules, and perform some basic maths to translate the copies.
>
>
Thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
>
University College London
>
> _SKELETAL TISSUE DYNAMICS GROUP_
>
_COMMITTEE MEMBER OF LONDON MATRIX GROUP _@LondonMatrixGrp
--
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Ph.D.
zsved...@biol.pmf.hr
web:
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