Hi Francois,
I really appreciate your explaining this all to me. I have used leap quite
a bit before, and so hopefully I should be fine now, with these
instructions.
Best regards,
Holly
On Fri, Sep 27, 2013 at 12:17 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Holly,
>
> > Thank you so much for your reply. I am afraid I am not familar with the
> > format on the REDD server links you sent me. Could you please tell me
> > which files I should download for the triphosphates?
>
> The 'format' is fully compatible with the t/xLEaP program; this means
> you need to know/learn how to use t/xLEaP.
>
> You need to download the entire package: see the bottom of the page
> http://q4md-forcefieldtools.org/REDDB/Project/F-90/F-90.tar.bz2
> or
> http://q4md-forcefieldtools.org/REDDB/Project/F-90/F-91.tar.bz2
>
> Then you need to read, modify & run the script1.ff file in t/xLEaP:
> See http://q4md-forcefieldtools.org/REDDB/Project/F-90/script1.ff
>
> perl -p -i.old -e 's/\#\#\!\# //g' script1.ff
> perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1.ff (strictly not needed)
> grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff
> tleap -f script1-new.ff
>
> More generally search for 'Now let's build the cofactors' in script1.ff
>
> dCMP1 = seq {P1M C5}
> dCMP2 = seq {P2M C5}
> dCDP1 = seq {P1M P1 C5}
> dCDP2 = seq {P2M P1 C5}
> dCTP1 = seq {P1M P1 P1 C5}
> dCTP2 = seq {P2M P1 P1 C5}
> dCQP1 = seq {P1M P1 P1 P1 C5}
> dCQP2 = seq {P2M P1 P1 P1 C5}
>
> CMP1 = seq {P1M D5}
> CMP2 = seq {P2M D5}
> CDP1 = seq {P1M P1 D5}
> CDP2 = seq {P2M P1 D5}
> CTP1 = seq {P1M P1 P1 D5}
> CTP2 = seq {P2M P1 P1 D5}
> CQP1 = seq {P1M P1 P1 P1 D5}
> CQP2 = seq {P2M P1 P1 P1 D5}
>
> You get CMP1 & CMP2 (x = 1, 2 - 2 terminal phosphates), CDPx, CTPx,
> CQPx, etc...
> same idea with the deoxy forms: dCMPx, dCDPx etc...
>
> I hope this helps...
>
> regards, Francois
>
>
>
> > On Thu, Sep 26, 2013 at 2:24 PM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> >> Dear Holly,
> >>
> >> > The structures that I am modelling include DCP (deoxy cytidine
> >> > triphosphate) and CTP (cytidine triphosphate). I can find the
> >> contributed
> >> > parameters for ATP and GTP on the AMBER website, but I don't see
> anything
> >> > for CTP or DCP. Can some one please recommend to me the best way to
> >> > parameterize these cofactors? Is it necessary for me to run a quantum
> >> > calculation on the molecules myself to get ESP fit charges?
> >>
> >> See http://q4md-forcefieldtools.org/REDDB/Project/F-90/ and/or
> >> http://q4md-forcefieldtools.org/REDDB/Project/F-91/
> >>
> >> & see the script1.ff LEaP script...
> >>
> >> We will propose a new version for these cofactors...
> >>
> >> regards, Francois
>
>
>
>
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>
>
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Received on Thu Sep 26 2013 - 23:30:04 PDT
