Hi Callum,
So it doesn't exist any program although it sounds like a common task that
many must have thought. Then I will write a script and share it here.
Best,
Thomas
On Sun, 10 Mar 2019 at 04:04, Dickson, Callum <callum.dickson.novartis.com>
wrote:
> Hi Thomas,
>
> You can look into RDKit: https://github.com/rdkit/rdkit
>
> Specifically, using the rdMolTransforms module you can print out bond
> lengths, angles and dihedrals for given atom indices.
>
> You can probably do a similar thing with mdtraj: http://mdtraj.org/1.9.0/
>
> However, you'd have to match the output (e.g. equilibrium bond length
> between certain atom pair) to gaff2 atom types. You can print out all atom
> indices and atom types for your ligand prmtop with ParmEd and the
> printDetails command to help with this.
>
> Best,
> Callum
>
>
> -----Original Message-----
> From: Thomas Evangelidis <tevang3.gmail.com>
> Sent: Friday, March 8, 2019 1:08 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] write equilibrium bond lengths, angles and dihedrals from
> a ligand structure file to a frcmod file
>
> Greetings,
>
> Is there any program that can read a structure file with an optimized
> ligand geometry and write the equilibrium bond lengths, angles, and
> dihedrals into a frcmod file? The frcmod file may pre-exist (created by
> parmchk2 script).
> I am doing high throughput MD simulations of thousands of protein-ligand
> complexes and I am not satisfied with the GAFF2 parameters for many of
> these ligands.
>
> Thanks in advance.
> Thomas
>
> --
>
> --
======================================================================
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <
https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <
https://www.ceitec.eu/>
Brno, Czech Republic
email: tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sun Mar 10 2019 - 04:00:02 PDT
