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TFE parameters
#3198 09/20/04 11:04 AM
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Hi,

can someone point my attention to parameters for
TFE(2,2,2-trifluoroethanol) to be used for simulations
with CHARMM of peptides in water/TFE?

Some ready made files for the topology/parameters?

Regards,


Leonardo De Maria Novozymes A/S Copenhagen-Denmark
Re: TFE parameters
ldemaria #3199 09/20/04 11:59 PM
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attached is a tar file that contains TFE parameters. also included are charmm22 protein toppar files and example inputs. the TFE parameters are in a toppar stream file that requires a special version of the protein toppar files that includes our revised LJ parameters for the alkanes. the test cases will give you an idea how to use the stream file.

alex

Attached Files
2859-toppar_tfe.tar.gz (0 Bytes, 1626 downloads)

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Re: TFE parameters
alex #3200 09/21/04 07:02 AM
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Thanks very much.


Leonardo De Maria Novozymes A/S Copenhagen-Denmark
Re: TFE parameters
ldemaria #3201 09/23/04 08:47 PM
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Alex,

I think your attachment got deleted in the upgrade of ubb. can you upload it again?

sorry about the problem,
Lee

Re: TFE parameters
alex #3202 09/29/04 01:56 PM
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Hi Alex,

I am interested in the TFE-parameters, as well.
Unfortunately, it really seems that the attachment
sent to Idemaria containing these parameters got
deleted - would it be possible to have the
attachment uploaded again (see request of hlwood)?

sorry for the problem also from my part

psaez

Re: TFE parameters
psaez #3203 10/01/04 02:18 PM
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i've added the tar file of the tfe parameters to my web page (see below) as well as attaching it to this post.

alex
http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

Attached Files
3088-toppar_tfe.tar.gz (0 Bytes, 7955 downloads)

School of Pharmacy
University of Maryland
20 Penn Street
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Re: TFE parameters
alex #3204 10/01/04 04:30 PM
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Thanks for having provided the TFE-parameters.

psaez

TFE parameter optimization
alex #3205 08/11/06 11:47 AM
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Dear "Parameter-Gurus", I used the (Jan '04) TFE parameters kindly provided by Alex M. for simulation of a 80% (v/v) TFE/water-mixture. There seem to be too little TFE-TFE interactions/H-bonds as compared to experimental data(e.g. J.Phys.Chem. A 2005, 109, 7667-7676) probably resulting from wrong F-atom parameters. Is anybody working on a new optimization of CHarmm TFE parameters ? Maybe I could join this effort based on our experiences with different boxes @ various TFE/water ratios (e.g. 4%, 20%, 40%, 60%, 14%, 30% and 80%[v/v]) mixtures. best regards, David

Re: TFE parameters
alex #3206 08/16/06 02:59 PM
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I am attching the pdb of ligand coumarin infact I wish to try with charmm(academic) fo this to create top and param files, as i saw the Example top and param for TFP- drug like molecule, it was split up in to several molecules and then at the end top file are created, similary how could i split my molecule to create top file accoding to the available charmm sources.
thanking you

Attached Files
11344-SARCOrigina153.pdb (0 Bytes, 558 downloads)
Re: TFE parameters
prakash #3207 08/20/06 12:17 AM
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there's a new tutorial on my web page that you will find helpful. alex


School of Pharmacy
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