Re: [AMBER] Help on understanding the errors

From: Dr. Anselm Horn <>
Date: Fri, 6 Nov 2020 11:48:47 +0100

Dear Ayesha,

the errors you posted indicate missing parameters for your ligand in the
standard library files and a potential problem with your mol2 file.

The general outline for your parameter generation task would be
(assuming it is an isolated organic ligand system):
1, Generate atomic charges of the minimized ligand system
You did this via RED server already.
2, Assign atom types for your system
Maybe the RED server provided you with suitable parameters here.
This atom type assignment is crucial, because from the ligand topology
and atom types the necessary parameters are derived to describe the
system in terms of the forcefield (bonds, angles, torsions, impropers).
3 Obtain missing parameters
If the atom type assignment leads to atom combinations, for which no
parameters are available in the library file, you have to provide/create
those missing parameters. parmchk2 does that task, i.e. it checks for
missing parameters and most often provides you with a suggestion for
missing ones. But you must check the output files.
4, Test
Run test MD simulations (e.g. of the isolated system) to ensure the
expected behaviour.

"ce" and "cf" are gaff atom types. Maybe they are present in your mol2 file?

Be sure that the "possibily open valence" error does not indicate an
error in your input structure (protonation state, total charge etc).

Maybe that helps.

All the best


On 11/06/2020 09:23 AM, Ayesha Fatima wrote:
> Dear all,
> Good morning. I am trying to build a ligand parameter file but running into
> contant errors. I need help in understanding the errors as I am not sure
> where they are coming from.
> I obtained a docked structure that I sent to the RED server for determining
> the charges. when I want to run it into tleap to create the topology and
> rst7 gives me the error "Possible open valence". after looking on
> the internet, I found I can turnoff the acdoctor and can do the .lib file
> by using the frcmod.known file from the server. When I want to build the
> p.prmtop and .rst7 files, it gives me the error
> ................................
> Building proper torsion parameters.
> Error: ** No torsion terms for ce-cf-ca-ca
> Error: ** No torsion terms for ce-cf-ca-ca
> Error: ** No torsion terms for ha-cf-ca-ca
> Error: ** No torsion terms for ha-cf-ca-ca
> Building improper torsion parameters.
> total 5 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Warning: Parameter file was not saved.
> ..............................................................................................
> I checked the error in the list archive where they say to build the frcmod
> file using parmchk.
> When I run that I get
>> parmchk -i ligand5.mol2 -f mol2 -o ligand5.frcmod
> Error: Error from the parser: syntax error
> ...............................
> I checked back its usage in the manual, I could not find where the problem
> is.
> Now my question is
> 1) what are these torsion term errors? when I checked the frcmod file,
> there are no "ce" and "cf" carbon atoms. are these some general terms?
> 2) when i want to run the parmchk, what is the syntax error. is it a wrong
> command line?
> I am using Amber18 and AmberTools18 in WSL installed in ASUS laptop with
> AMD Ryzen5 processor.
> Your help is really appreciated.
> Thank you
> Ayesha Fatima
> _______________________________________________
> AMBER mailing list

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Received on Fri Nov 06 2020 - 03:00:02 PST
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