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
Factor).
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.
Charalampos
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Received on Mon Sep 02 2019 - 03:00:04 PDT
