CHARMM Development Project
Posted By: ldemaria TFE parameters - 09/20/04 11:04 AM
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,
Posted By: alex Re: TFE parameters - 09/20/04 11:59 PM
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 File
2859-toppar_tfe.tar.gz  (1626 downloads)
Posted By: ldemaria Re: TFE parameters - 09/21/04 07:02 AM
Thanks very much.
Posted By: hlwood Re: TFE parameters - 09/23/04 08:47 PM
Alex,

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

sorry about the problem,
Lee
Posted By: psaez Re: TFE parameters - 09/29/04 01:56 PM
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
Posted By: alex Re: TFE parameters - 10/01/04 02:18 PM
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 File
3088-toppar_tfe.tar.gz  (7955 downloads)
Posted By: psaez Re: TFE parameters - 10/01/04 04:30 PM
Thanks for having provided the TFE-parameters.

psaez
Posted By: greenhorn TFE parameter optimization - 08/11/06 11:47 AM
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
Posted By: prakash Re: TFE parameters - 08/16/06 02:59 PM
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 File
11344-SARCOrigina153.pdb  (558 downloads)
Posted By: alex Re: TFE parameters - 08/20/06 12:17 AM
there's a new tutorial on my web page that you will find helpful. alex
Posted By: alex Re: TFE parameter optimization - 08/20/06 12:19 AM

TFE a tricky molecule. the condensed phase properties are not ideal; however, I am currently not working on them.

alex
Posted By: greenhorn Re: TFE parameters - 08/21/06 12:17 AM
Dear Alex,

many thanks for your new ressources on your homepage !
...is it possible that it does not make sense to try to optimize a 2,2,2trifluoroethanol molecule model for the (current) additive Charmm force field in stead of waiting for the next generation of force fields that will allow for explicit representation of polarization effects (which could be expected to be quite important in 2,2,2trifluoroethanol/water mixtures as fluor atoms are extremely electrophilic)? If not: how much time would you say is necessary if I start as a beginner in parametrization
to build a more suitable TFE model for building good TFE/water boxes which can reproduce experimental properties more accurately ?

many thanks for your response in advance,
David
Posted By: prakash other then TFE parameters - 08/21/06 06:51 PM
It would be easier if i have informations other then TFE.
Posted By: alex Re: TFE parameters - 08/29/06 01:20 AM

it will take a good amount of time as you will need to do a careful optimization of the LJ parameters, which is the most difficult aspect of the FF to optimize. I suggest you take the current model and do condensed phase simulations in different conditions for which experimental data is available. the absolute values for the empirical model may not be correct, but if you are getting the trends correct, that should be adequate for your needs.

alex
Posted By: prakash model_b_molvib_g03.inp shows error - 08/30/06 09:21 PM
In the tutorial of forcefiled parameters for new molecules, where i could run all the inp files except model_b_molvib_g03.inp and showing an error

charmm/c32b1/exec/gnu/charmm < model_b_molvib_g03.inp > model_b_molvib_g03.out
fmt: end of file
apparent state: unit 12 named fort.12
last format: (20A4)
lately reading sequential formatted external IO
Abort

how could i rectify it and how to see the optimized charges.

thank you
Posted By: prakash parameter request - 09/04/06 09:19 PM
Dear all

How could i start this molecule (attchement)to create topology file with exisiting topolgy information (analogy model) i couldnt find more examples on this topic.
thanking you

Attached picture 11518-lastfigurec153.jpg
Posted By: Lauren Re: parameter request - 01/11/19 03:55 AM
Hi all,

I realise this discussion is quite old but I would just like to ask if there are any recent TFE parameters that you can recommended for use with CHARMM force fields? Specifically as a solvent.

Thanks in advance for the help.

Lauren
Posted By: rmv Re: parameter request - 01/11/19 04:31 AM
Have you checked the CGenFF topology file, top_all36_cgenff.rtf?
Posted By: Lauren Re: parameter request - 01/18/19 07:12 AM
Dear Rick,

Thank you! I didn't realise I could find it there.

Thanks a lot,

Lauren
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