Re: [AMBER] cytidine triphosphate

From: FyD <>
Date: Fri, 27 Sep 2013 08:17:58 +0200

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

Then you need to read, modify & run the script1.ff file in t/xLEaP:

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 <> 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 and/or
>> & see the script1.ff LEaP script...
>> We will propose a new version for these cofactors...
>> regards, Francois

AMBER mailing list
Received on Thu Sep 26 2013 - 23:30:03 PDT
Custom Search