[AMBER] Error creating topology and coordinates file

From: <charalamm.cheng.auth.gr>
Date: Mon, 02 Sep 2019 12:42:20 +0300

Hello everyone,

I want to perform MM/GBSA and MM/PBSA analysis using trajectories
created from Desmond. As far as I know, I have to create coordinates
and topology files for the complex, the ligand (which in my case is
DNA oligo) and the protein ( which in my case is a Transcription

My method until now is to take the file-in.cms from Desmond remove the
waters and the ions and then export the pdb. Then I pass this pdb to
tleap to export the topology and the coordinates file.

$ tleap
> source leaprc.protein.ff14SB
> source leaprc.DNA.OL15
> PDB = loadpdb complex.pdb
Loading PDB file: ./complex.pdb
Created a new atom named: OXT within residue: .R<ASP 313>
Created a new atom named: H2 within residue: .R<PRO 314>
Created a new atom named: H3 within residue: .R<PRO 314>
   total atoms in file: 9906
   The file contained 3 atoms not in residue templates

> saveamberparm PDB TOP.prmtop CORD.rst7
At this step the following error occurs:
Checking Unit.

Warning: There is a bond of 84.639821 angstroms between:

Warning: The unperturbed charge of the unit (-36.000000) is not zero.
FATAL: Atom .R<ASP 313>.A<OXT 13> does not have a type.
FATAL: Atom .R<PRO 314>.A<H2 15> does not have a type.
FATAL: Atom .R<PRO 314>.A<H3 16> does not have a type.

Error: Failed to generate parameters

Warning: Parameter file was not saved.

Is there a way to fix it or is there another way to create the
topology and coordinates files?

Thank you very much!

My best regards.

AMBER mailing list
Received on Mon Sep 02 2019 - 03:00:04 PDT
Custom Search