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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Received on Thu Sep 26 2013 - 23:30:03 PDT
