Dear Bill,
I tried again using just the loadamberprep command as you suggested. it
worked fine.
Thank you
regards
On Fri, Nov 6, 2020 at 7:14 PM Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> 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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>> >>>
>> >>
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Received on Fri Nov 06 2020 - 03:30:05 PST
