Hello Jason,
I am attaching all the input and output files for your kind consideration.
My objective is to simulate the modified ribonucleoside 2-thiouridine (2SU
or s2U) with the FF99CHI. The FF99CHI was proposed by Yildirim et al. (
http://pubs.acs.org/doi/abs/10.1021/ct900604a).The parameters for modified
nucleosides was developed by Santa Lucia et al. (
http://pubs.acs.org/doi/abs/10.1021/ct600329w).
I found the FF99CHI for normal nucleosides is working good. But I want to
check it for modified residues.
There is no error message in the output file. The nucleoside is a neutral
system. So please check the files and let me know whether it is working or
not ! It will be a great help.
I am afraid that if it is possible to apply FF99CHI for modified nucleoside
also.
Thanks
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Fri, Dec 14, 2012 at 6:25 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Dec 14, 2012 at 2:38 AM, Indrajit Deb <biky2004indra.gmail.com
> >wrote:
>
> > Dear amber users,
> >
> > Is it ok with the following script for tleap to use the parameter files
> > developed by Santa Lucia Group with FF99CHI force field developed by
> > Yildirim et al. ?
> >
>
> Does your script work? Does it give you what you want? If yes to both,
> then yes, your script is OK. If no to either, then no, your script is not
> OK.
>
> You will get more useful answers with more specific questions. It's not
> worthwhile to comb through a script we can't execute to see if we can find
> any mistakes (e.g., a computer will find the typo 'loadpbd' faster than we
> will, if we do at all) -- tleap can do that faster than us. Since we don't
> have your files, we have no way of knowing whether you've forgotten
> anything (were there any linkages, like disulfide bonds if you have protein
> residues, is your system actually positively charged so you should have
> added Cl- ions, do you have any custom residues you need to separately load
> parameter files and library files for, etc.)
>
> tleap will not fail quietly. If you've done something 'wrong', most likely
> you will get a host of error messages (all of which you can google at this
> point to find suitable solutions for, most likely). If a topology file is
> written successfully, I suggest loading the resulting files into a
> visualization program (e.g., VMD) and taking a look at the structure to
> make sure it seems sensible.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Fri Dec 14 2012 - 11:30:04 PST
