Re: [AMBER] charge in constant redox cein file vs. prmtop file

From: Feng, Zimin <Feng.Zimin.hydro.qc.ca>
Date: Wed, 24 Apr 2019 18:10:41 +0000

Ah! Checking %flag charge is exactly what I did :P
Thanks for letting me know... should have been more careful.
Thanks!


De : Cruzeiro,Vinicius Wilian D [mailto:vwcruzeiro.ufl.edu]
Envoyé : 24 avril 2019 12:51
À : Feng, Zimin
Cc : AMBER Mailing List
Objet : Re: charge in constant redox cein file vs. prmtop file


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Hello Zimin,

Thanks for sending these files. Actually, the charges in the prmtop are identical to the charges of state 0 in the cein file. I suspect where the confusion might be coming from. Are you by any chance manually opening the prmtop file and checking for "%FLAG CHARGE"? If so, the charge units in the prmtop file are different (the charge of one electron is not 1 there). In order to see the charges in the same units as in the cein file, you need to open the prmtop file in parmed: parmed -p mp8_is.prmtop . Once inside parmed type: printDetails :HEH

If you would like to see the charges of all states that should be inside your cein file in a more organized way type: ceinutil.py --describe HEH

I hope this helps,
All the best,


Vinícius Wilian D. Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

________________________________
From: Feng, Zimin <Feng.Zimin.hydro.qc.ca>
Sent: Wednesday, April 24, 2019 12:14 PM
To: Cruzeiro,Vinicius Wilian D
Cc: AMBER Mailing List
Subject: RE: charge in constant redox cein file vs. prmtop file


Hi Vinicius,

Sure here they are in the attachment. And yes the charges of HEH residue differ in both files as well, nether redox state matches that found in prmtop.

Best regards,

Zimin





De : Cruzeiro,Vinicius Wilian D [mailto:vwcruzeiro.ufl.edu]
Envoyé : 23 avril 2019 18:52
À : Feng, Zimin
Cc : AMBER Mailing List
Objet : Re: charge in constant redox cein file vs. prmtop file



Courriel provenant de l'externe
ATTENTION, avant d'accéder à une pièce jointe ou à un lien de ce courriel, assurez-vous que celui-ci provient d'un tiers de confiance.

Hello Zimin,



Could you please send the prmtop and cein files you mentioned so I can take at look at the discrepancies you are talking about? Also, are you referring to the charges of the HEH residue?



Now answering your last question: once the constant redox potential simulation starts, the charges are overwritten by the set of charges obtained from the cein file. Different redox states have different charge distributions in the cein file.



All the best,



Vinícius Wilian D. Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

________________________________

From: Feng, Zimin <Feng.Zimin.hydro.qc.ca>
Sent: Tuesday, April 23, 2019 6:03 PM
To: Cruzeiro,Vinicius Wilian D
Cc: AMBER Mailing List
Subject: charge in constant redox cein file vs. prmtop file



Hi Vinicius or anyone who's familiar with it,



I noticed that the charges in cein file and the charges in prmtop file don't really match. This is the case even in the tutorial example.

Is it acceptable? My guess is that prmtop file's charge is overwritten by cein? Or the charges in cein was used for redox transition only and prmtop charge is used for the rest of the evolution?



Thank you in advance!



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Zimin Feng

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Received on Wed Apr 24 2019 - 11:30:03 PDT
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