rxn in tpl

[fedaaali]

I am trying to create tpl for ions such as Zr, Cd, how could I calculate the rxn entry in the tpl ? I tried the method written here but it doesn't give me correct values when I tried to remake tpl for existing ions ?

[mrgunner]

Can you tell us what numbers you are getting and what you expect or shoot us back a tpl file.

On Apr 28, 2019, at 7:19 PM, fedaaali notifications@github.com wrote:

I am trying to create tpl for ions such as Zr, Cd, how could I calculate the rxn entry in the tpl ? I tried the method written here but it doesn't give me correct values when I tried to remake tpl for existing ions ?

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[mrgunner]

The things that effect this are Ion radius Charge Inner dielectric constant (are you using 8 or 4?). Also if you are using 4 you need a param04 directory for the tpl files. If you use 8 it lols for param08

On May 9, 2019, at 7:43 AM, noname notifications@github.com wrote:

for example, the rxn that I am getting for the Zn ion is -56.875 and I am expecting it to be -91.248 as in the original one.

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[fedaaali]

thx Dr Gunner for your reply and clear explanation, now I am getting the correct rxn value for the Zn.

[fedaaali]

the radius that is written in the tpl isn't the VDW radius?

[mrgunner]

It’s the radius for the delphi making of protein (inside dielectric constant) and outside (e=80)

for salvation energy if you turn the salt off the reaction field energy can be computers analytically

∆Gsolv = q^2/(2r) [1/ein -1/eout\ https://en.wikipedia.org/wiki/Born_equation

the vdw radii are in always_needed.tpl and they are used for the molec mechanic calc of explicit atoms touching each other

On May 9, 2019, at 5:21 PM, noname notifications@github.com wrote:

the radius that is written in the tpl isn't the VDW radius?

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[fedaaali]

Thanks a lot for your precious help. I'm really grateful.

[mrgunner]

Good luck. Let us know if you get something good out of it.

On May 10, 2019, at 2:38 PM, noname notifications@github.com wrote:

Thanks a lot for your precious help. I'm really grateful.

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[fedaaali]

Dear Dr Gunner, I am facing problem regarding calculating the pka and I can't even understand what is it !! I and my supervisor are calculating the pka for the same files, but I am getting totally different results!! we are using the same tpls and pdbs! I tried many times and I can't figure out what is the problem! could you help me figuring out what might be the problem !

[mrgunner]

I think we need to talk. Are you in John’s lab? Can you zip up the directory?

On May 19, 2019, at 8:30 PM, noname notifications@github.com wrote:

Dear Dr Gunner, I am facing problem regarding calculating the pka and I can't even understand what is it !! I and my supervisor are calculating the pka for the same files, but I am getting totally different results!! we are using the same tpls and pdbs! I tried many times and I can't figure out what is the problem! could you help me figuring out what might be the problem !

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[fedaaali]

Dear Dr Gunner, Thanks for your reply, I am studying in Egypt. yea for sure, I will upload it today

Thanks a lot

[fedaaali]

Dear Dr.Gunner, here is the version that I am using and one of the files that I am trying to calculate the pka for ( aqua manganese ) mcce2.5.zip

Mn.zip

[mrgunner]

To help you more I would like to know your name and what lab you are working in. Also please let me know what system you are working on and what it is the question.
These will help answer your questions in a more efficient way. Marilyn

On May 20, 2019, at 2:02 PM, noname notifications@github.com wrote:

Gunner, here is the version I am using and one the files that I am trying to calculate ( aqua manganese )

Mn.zip https://github.com/choderalab/mcce-charges/files/3199174/Mn.zip mcce2.5.zip https://github.com/choderalab/mcce-charges/files/3199176/mcce2.5.zip — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/choderalab/mcce-charges/issues/62?email_source=notifications&email_token=ACNU6XXETHERN3VQNRZSXRDPWLRSRA5CNFSM4HI7TBEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVZTVXI#issuecomment-494090973, or mute the thread https://github.com/notifications/unsubscribe-auth/ACNU6XXDMXRTGF25T7JDS7DPWLRSRANCNFSM4HI7TBEA.

[fedaaali]

sorry for being late .. my name is fedaa ali and I am working in material science lab at Zewail city in Egypt. I am working on linux system (Ubuntu 18), I am getting different values for the pkas for aqua metals from that calculated by my supervisor. we are using same tpls and same pdbs. so my question is could you help me to figure out the problem ?

[mrgunner]

Who is your supervisor?
What metals. Please your replies are too vague.

On May 25, 2019, at 11:36 AM, noname notifications@github.com wrote:

sorry for being late .. my name is fedaa ali and I am working in material science lab at Zewail city in Egypt. I am working on linux system (Ubuntu 18), I am getting different values for the pkas for aqua metals from that calculated by my supervisor. we are using same tpls and same pdbs. so my question is could you help me to figure out the problem ?

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[fedaaali]

he is Dr. Muhammad Amin Assistant Professor of Physics at University of Groningen, I am working on different aqua metals for example...[mn(h2o)6]^2 I am trying to calculate the pkas of water molecules. my issue is that I am getting different values from that is calculated by Dr. Muhammad
sorry for any inconvenience

[mrgunner]

Thank you. I know Dr Amin very well.
I will ask Divya to help you. She is collaborating with Muhamed and uses the techniques developed when Muhamed was in my lab.

On May 27, 2019, at 7:23 AM, noname notifications@github.com wrote:

he is Dr. Muhammad Amin Assistant Professor of Physics at University of Groningen, I am working on different aqua metals for example...[mn(h2o)6]^2 I am trying to calculate the pkas of water molecules. my issue is that I am getting different values from that is calculated by Dr. Muhammad sorry for any inconvenience

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[fedaaali]

Thank you very much