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Re: Androstenedione parameters
rmv #25666 10/22/10 03:17 PM
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Manori Offline OP
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Dear Kenno,

Can I use your parameters for phenylmethylketone to start parametrize the butenone? It would be great if you could let me know whether you could share it with me. Or else direct me to a good compound which is already in the database to begin with.

Thanks

Manori

Re: Androstenedione parameters
Manori #25667 10/22/10 04:36 PM
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Originally Posted By: Manori
4) Since cholesterol has different atom types how should I put it in the cgenff files.
Actually, there's a cholesterol topology in CGenFF as well so you can represent your entire molecule with CGenFF.

I would recommend doing a full parameterization - charges, equilibrium geometry, vibrations and potential energy scan - on butenone, (or, for even better accuracy and transferability, cis and trans 3-penten-2-one, as suggested by rmv). Must-reads before doing this are:
  • The CGenFF paper
  • The CGenFF tutorial
  • The CGenFF FAQ
  • Poker's molvib tutorial
  • Threads by various people on this forum who have successfully parameterized molecules


An experienced CGenFF worker can get through the whole parameterization procedure in one or two days. However, the first time usually takes much longer, about two weeks on average. And that's for people working in our group; if your only source of support is this forum, it may easily take you 3 or 4 weeks. I'm telling you this because the enone moiety is actually on the to-do list of a grad student in our lab. It's very difficult for me to estimate when she will be done with it because my boss can give her a different and urgent assignment any time, but if nothing goes wrong, she might be finished with it by the beginning of December. So you have the choice between committing a few weeks to this parameterization and be reasonably sure to have your parameters somewhere mid or end November, or gambling that everything will work out well at our end and that you will get the parameters from us by mid-December (but I have to stress again that I can make no guarantees whatsoever).

Re: Androstenedione parameters
Kenno #25688 10/26/10 06:45 PM
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Let me know what your decision is. If you are going to do the parametrization yourself, I can pull together the phenylmethylketone parameters for you to use as initial guess.

Re: Androstenedione parameters
Kenno #25690 10/27/10 09:20 PM
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Manori Offline OP
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Dear Kenno,

I am going to start parametrize butenone. Once your graduate student finish the job please send me the data. Then I can compare to see my capabilities. I would be grateful if you could give me the initial para for this. Also, I have a difficulty of determining what atom types to use for the double bonded carbon in butenone. Can I use CG2RC7 for the double bonded carbon? It would be great if you could give a hint on this.

Thanks for all the valuable advice and help


Manori

Last edited by Manori; 10/28/10 03:54 AM.
Re: Androstenedione parameters
Manori #25691 10/27/10 09:45 PM
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Dear Kenno,

Why we need to parametrize both cis and trans of 3-penten-2-one? I thought the cis conformation gives a half of the ring and it is what we need to do. I do not understand why need trans.

Thanks

Manori

Re: Androstenedione parameters
Manori #25701 10/28/10 05:31 PM
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Start with butenone. I ran it through the automatic assignment program, then replaced select charges and parameters with values from phenyl methyl ketone. The atom types in this file are correct; the charges and parameters should be considered an "initial guess". The most important thing to re-optimize is the rotatable C2-C3 dihedral.

Attached Files
beon_adjusted.str.txt (2.93 KB, 305 downloads)
Re: Androstenedione parameters
Kenno #25703 10/28/10 06:37 PM
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Thank you very much for your help. I am going to go ahead and use this as a initial para for butenone. I am thinking of doing a full optimization of charge, bonds and angles, and the c2-C3 dihedral. Please tell me is there anything specifically that I need to keep in mind when I am doing this.

Thanks again.

Manori

Re: Androstenedione parameters
Manori #25706 10/29/10 04:24 PM
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Actually, it would be an advantage if you could keep all charges except C2, O2 and C3 at their standard values during charge optimization, if the water interactions are not too bad (if they are, changing C4 can be considered). This is not set in stone, but it would make life somewhat easier when moving to the larger compounds.

Otherwise, the compound should be pretty regular and well-behaved.

Re: Androstenedione parameters
Kenno #26002 12/14/10 05:51 PM
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We optimized butenone (BEON) and added it to the new 2b6 release of CGenFF. I will make an formal announcement on these forums tomorrow, but you can already download it here.

Re: Androstenedione parameters
Kenno #26028 12/21/10 12:41 AM
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As for the larger model compounds, you can submit them to the CGenFF program an see how high the penalties are. This is a very convenient way to assess how well a given molecule is supported by CGenFF, and which parts of the molecule are most in need of optimization.

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