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 Mon Jul 19 2021 - 05:30:02 PDT
