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#606 11/29/03 02:50 PM
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jb007 Offline OP
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Dear all,
I have a high interest in using implicit solvation models implemented in CHARMM. However, being an amateur in this field I I'd like to know more about performances in CHARMM in general, and the Generalized Born Molecular Volume approach in particular. For the latter, I've tried to do single-point energy calculations with the analytical approach, but have encountered some syntactic problems, and therefore I ask for a sample input file concerning a protein-DNA system, and using the 27 all atom rtf/param set.

Thanks!

Johan


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cao Offline
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Did you ever check $charmm_home/test/c27test/genborn22.inp?

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jb007 Offline OP
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Yes,
I've looked through all test-cases (always the first thing to do), but I want to learn more about the GB Molecular Volume method, since it is claimed to work on any force-field. In particular, I'm interested in the analytical approach and I've already tried the first and second methods of GBMV.

Johan

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jb007 Offline OP
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Are you experienced with implicit solvation techniques? I have some problems with charged systems in this aspect, so if you know how to work-around such problems, I'd really be happy to know.

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cao Offline
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I am sorry, I am not experienced with them. Actually, I just used GB recently, and my personal IMMATURE understanding is:
GB model is mainly to attain quantitative agreement with PB results. And even for such a simple goal, it is still parameterized to attain it. The GB formula, to me, is doubtful.

Therefore, I gave up GB. And since PB is not expensive to my problems, I am using PB.

I think we need get comments from those more experienced persons.

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jb007 Offline OP
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Yes,
but the GBMV method (in c30a1) gives more "reasonable" results, but I'll probably have to resort to PB as well . Are you experienced in treating metals within the framework of PB?

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cao Offline
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Maybe GBMV is better, I am using c29b2, :-(
Sorry, I don't have experience of dealing with metals. There some some useful information on professor Benoit Roux 's website.


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