Hi Indrajit -
You should be able to do what you are proposing. The only issue is with
the residue 2SU and s2U. The chi torsions are not revised for those
residues, and therefore the chi parameters of uridine might not reflect
the real potential surface for either 2SU or s2U. Yet, I think you can
still use the chi parameters (revised for uridine) on 2SU and s2U.
There are a couple of issues with your system:
1. The file 2SU.prepin does not have the right atom type for atom name C6.
If you are going to use revised Uridine chi parameters, you have to
replace atom type CM to C4 for atom name C6.
replace
23 C6 CM S 22 20 19 1.328 118.937 0.045 -0.14387
to
23 C6 C4 S 22 20 19 1.328 118.937 0.045 -0.14387
2. Your S2 atom is bound to C2 and the atom type for C2 is CA. You will
need to add a couple of new terms to your frcmod file. The following
angular and torsional terms are missing:
CA-N*-C4
NA-CA-N*-C4
SS-CA-N*-C4
You might need to add another improper term for S2 atom (so that it stays
planar).
3. Your xleap .in file should be something like that:
-------------------------------------------------------
source oldff/leaprc.rna.ff99
addAtomTypes {
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
{ "C3" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "C7" "C" "sp2" }
{ "C8" "C" "sp2" }
}
loadamberparams frcmod.parmCHI
loadamberparams 2SU.frcmod
loadamberprep 2SU.prepin
verbosity 2
S=loadpdb na_server_s2u.pdb
saveamberparm S na_server_s2u.prmtop na_server_s2u.inpcrd
----------------------------------------------------------
Hope this helps. Good luck,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Fri, 14 Dec 2012, Indrajit Deb wrote:
>
> 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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
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Received on Fri Dec 14 2012 - 12:00:01 PST
