> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Fri Nov 06 2020 - 03:30:03 PST
