Thank you Bill. It is LIG
I again did some troubleshooting and reconverted the .prep file to mol2 and
followed all the steps again using the frcmod file i created with the .prep
file. So now it all went ok and I got the ligand topology. no "open
valence" issue also this time.
Thank you all for your help. i run the md simulation and see if all goes
well.
Thank you once again
Ayesha
On Fri, Nov 6, 2020 at 7:06 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> > LIG = loadamberprep lig-red.prep
>
> The loadamberprep cmd gets the residue name from the file, so 'LIG =' is
> effectively ignored. What's the res name in the file?
>
> Bill
>
> On 11/6/20 3:02 AM, Ayesha Fatima wrote:
> > 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
> >>> _______________________________________________
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> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
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Received on Fri Nov 06 2020 - 03:30:04 PST
