Thank you Anselm for your email
I resolved the matter to some extent by doing way. I used antechamber to
create a .prep file instead of a mol2 file. then I used this prep file to
make the frcmod file which indeed gave me the "ce and"cf" parameters.
Now I have another issue which seems silly but not sure what is wrong. i
want to create the .lib file but it gives error. My commands go like this
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
tleap -f leaprc.protein.ff14SB
source leaprc.gaff
> LIG = loadamberprep lig-red.prep
Loading Prep file: ./lig-red.prep
> loadamberparams frcmod.lig-red
Loading parameters: ./frcmod.lig-red
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> saveoff LIG lig-red.lib
Error: saveOff: Argument #1 is type String must be of type: [unit
parameter_set list]
usage: saveOff <object> <filename>
-----------------------------------------------------------
any idea?
Thank you
Ayesha
On Fri, Nov 6, 2020 at 6:49 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> 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
>
> Anselm
>
>
>
>
>
> 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 file.it 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 06 2020 - 03:00:03 PST
