Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
TFE parameters
#3198 09/20/04 11:04 AM
Joined: Jun 2004
Posts: 8
Forum Member
OP Offline
Forum Member
Joined: Jun 2004
Posts: 8
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
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782
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, 1621 downloads)

School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: TFE parameters
alex #3200 09/21/04 07:02 AM
Joined: Jun 2004
Posts: 8
Forum Member
OP Offline
Forum Member
Joined: Jun 2004
Posts: 8
Thanks very much.


Leonardo De Maria Novozymes A/S Copenhagen-Denmark
Re: TFE parameters
ldemaria #3201 09/23/04 08:47 PM
Joined: Sep 2003
Posts: 119
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 119
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
Joined: Sep 2004
Posts: 2
P
Forum Member
Offline
Forum Member
P
Joined: Sep 2004
Posts: 2
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
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782
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, 7951 downloads)

School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: TFE parameters
alex #3204 10/01/04 04:30 PM
Joined: Sep 2004
Posts: 2
P
Forum Member
Offline
Forum Member
P
Joined: Sep 2004
Posts: 2
Thanks for having provided the TFE-parameters.

psaez

TFE parameter optimization
alex #3205 08/11/06 11:47 AM
Joined: May 2006
Posts: 11
G
Forum Member
Offline
Forum Member
G
Joined: May 2006
Posts: 11
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
Joined: Oct 2005
Posts: 206
P
Forum Member
Offline
Forum Member
P
Joined: Oct 2005
Posts: 206
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, 552 downloads)
Re: TFE parameters
prakash #3207 08/20/06 12:17 AM
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782
there's a new tutorial on my web page that you will find helpful. alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: TFE parameter optimization
greenhorn #3208 08/20/06 12:19 AM
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782

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

alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
Re: TFE parameters
alex #3209 08/21/06 12:17 AM
Joined: May 2006
Posts: 11
G
Forum Member
Offline
Forum Member
G
Joined: May 2006
Posts: 11
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

other then TFE parameters
alex #3210 08/21/06 06:51 PM
Joined: Oct 2005
Posts: 206
P
Forum Member
Offline
Forum Member
P
Joined: Oct 2005
Posts: 206
It would be easier if i have informations other then TFE.

Re: TFE parameters
greenhorn #3211 08/29/06 01:20 AM
Joined: Oct 2003
Posts: 782
A
Forum Member
Offline
Forum Member
A
Joined: Oct 2003
Posts: 782

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


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201
model_b_molvib_g03.inp shows error
alex #3212 08/30/06 09:21 PM
Joined: Oct 2005
Posts: 206
P
Forum Member
Offline
Forum Member
P
Joined: Oct 2005
Posts: 206
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

parameter request
alex #3213 09/04/06 09:19 PM
Joined: Oct 2005
Posts: 206
P
Forum Member
Offline
Forum Member
P
Joined: Oct 2005
Posts: 206
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 Files
11518-lastfigurec153.jpg (0 Bytes, 548 downloads)
Re: parameter request
ldemaria #37264 01/11/19 03:55 AM
Joined: Jan 2019
Posts: 2
L
Forum Member
Offline
Forum Member
L
Joined: Jan 2019
Posts: 2
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

Re: parameter request
ldemaria #37265 01/11/19 04:31 AM
Joined: Sep 2003
Posts: 8,504
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,504
Have you checked the CGenFF topology file, top_all36_cgenff.rtf?


Rick Venable
computational chemist

Re: parameter request
ldemaria #37291 01/18/19 07:12 AM
Joined: Jan 2019
Posts: 2
L
Forum Member
Offline
Forum Member
L
Joined: Jan 2019
Posts: 2
Dear Rick,

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

Thanks a lot,

Lauren

Page 1 of 2 1 2

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.022s Queries: 56 (0.012s) Memory: 1.0733 MB (Peak: 1.2847 MB) Data Comp: Off Server Time: 2020-10-24 17:14:51 UTC
Valid HTML 5 and Valid CSS