Re: [AMBER] Error creating topology and coordinates file

From: <>
Date: Mon, 02 Sep 2019 12:58:21 +0300

An Update:
Deleting the lines in the pdb containing those atoms and repeating the
process creates the topology and coordinates files normally but I am
not sure if I should do this as I am new to molecular dynamics
My original pdb file is 1RAM.

So my extra question is if it is alright to just delete them?

Thank you,


> 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 - 03:00:05 PDT
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