Re: [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file

From: Dickson, Callum <callum.dickson.novartis.com>
Date: Sun, 10 Mar 2019 03:03:29 +0000

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://urldefense.proofpoint.com/v2/url?u=https-3A__www.uochb.cz_web_structure_31.html-3Flang-3Den&d=DwICAg&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=1cb4YqxPyhGduS6UEYk0DDIxOs_-CeUPcWPcFhqx0kY&s=TzPgMrAzLLXzz5IhrLybSNIcK8UH3VlpULU_8coLpdE&e=>
Prague, Czech Republic
  &
CEITEC - Central European Institute of Technology <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ceitec.eu_&d=DwICAg&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=1cb4YqxPyhGduS6UEYk0DDIxOs_-CeUPcWPcFhqx0kY&s=-Zns-qsI4hNLN9qqDPg9DhNUc6_uHF6mGkLg-dO8gXo&e=>
Brno, Czech Republic
email: tevang3.gmail.com
website: https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.com_site_thomasevangelidishomepage_&d=DwICAg&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=1cb4YqxPyhGduS6UEYk0DDIxOs_-CeUPcWPcFhqx0kY&s=skzk3Aw9cGfTx1ChCbMrX_YjAcZPX5zBIASUMRWt7DM&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=1cb4YqxPyhGduS6UEYk0DDIxOs_-CeUPcWPcFhqx0kY&s=6dyWCnnI3BPwDjQ9-yH0xjWPhQUAJxqrHGd8DDXYIj8&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 09 2019 - 19:30:02 PST
Custom Search