I have my own prmtop write to create an input forcefield to pmemd. I could find all the necessary information to parameterize the protein / ligand from the forcefield files provided in the dat folder of the amber installation. The only section I can’t write is the RADII and SCREEN section to fully support all GB modes. I would like to know where tleap looks to write this section. Where do these numbers come from? Which parameter files are read to fill the section with the appropriate values for the corresponding atom types. We cannot depend on the amber tools and hence are trying to write a fully compliant prmtop file.
In the source code you gave me I couldn’t find any SCREEN value 0.79, 0.72 or 0.85. So I am still puzzled how tleap gets these exact numbers.
> On Jul 19, 2021, at 8:14 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> I'm not understanding the problem, the radii are listed in the text you
> quoted. Different parameters may be in different places, for example the
> radii are in the prmtop (these are chosen in theeap input, they are not
> specific to a certain gb model) and the screening parameters are in the
> source code that I gave before.
>
> On Mon, Jul 19, 2021, 8:07 AM Maximilian Ebert <max.ebert.me.com> wrote:
>
>> Thanks for the answer. I looked at the file but I can’t find the numbers I
>> see for Alanine in the prmtop when created via tleap:
>>
>> ….
>> 0
>> %FLAG RADIUS_SET
>>
>> %FORMAT(1a80)
>>
>> modified Bondi radii (mbondi)
>>
>> %FLAG RADII
>>
>> %FORMAT(5E16.8)
>>
>> 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
>> 1.70000000E+00
>> 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
>> 1.50000000E+00
>> 1.50000000E+00
>> %FLAG SCREEN
>>
>> %FORMAT(5E16.8)
>>
>> 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
>> 7.20000000E-01
>> 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
>> 8.50000000E-01
>> 8.50000000E-01
>> %FLAG IPOL
>>
>> %FORMAT(1I8)
>>
>> 0
>> …
>>
>> What am I missing? I found the constants alpha, beta, etc. but not the
>> values for SCREEN + RADII necessary for OBC GB.
>>
>> Thanks
>>
>>> On Jul 13, 2021, at 4:27 PM, Carlos Simmerling <
>> carlos.simmerling.gmail.com> wrote:
>>>
>>> look at mdin_ctrl_dat.F90 in src/pmemd/src.
>>> they are also written to the mdout file at the beginning of the run.
>>>
>>>
>>> On Tue, Jul 13, 2021 at 2:27 PM Maximilian Ebert <max.ebert.me.com>
>> wrote:
>>>
>>>> Thanks, but is there any text file with the parameters or do they exist
>>>> only within the parmed code?
>>>>
>>>>> On Jul 7, 2021, at 4:26 PM, David A Case <david.case.rutgers.edu>
>> wrote:
>>>>>
>>>>> On Wed, Jul 07, 2021, Maximilian Ebert wrote:
>>>>>
>>>>>> For GB in AMBER the screen/radii section in prmtop files is necessary
>> in
>>>>>> some modes. Where do I find the parameters in $AMBERHOME/dat to put
>> into
>>>>>> these sections? I simply can’t find the origin of the data if the
>>>> general
>>>>>> born screening parameters.
>>>>>
>>>>> You can get these by using the "changeRadii" command in parmed.
>>>>>
>>>>> ...good luck...dac
>>>>>
>>>>>
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Received on Tue Jul 20 2021 - 05:30:02 PDT
