Re: [AMBER] ATP and Mg2+ parameters

From: FyD <>
Date: Tue, 15 Jul 2014 13:05:20 +0200

Dear Valentina,

> I looked at but
> it was not really clear to me what are parameters for ATP.

  & read

perl -p -i.old -e 's/\#\#\!\# //g' script1.ff
grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff

tleap -f script1-new.ff

search for "# 1) Let's start by AMP, ADP, ATP, AQP and even more..."

dAMP1 = seq {P1M A5}
dAMP2 = seq {P2M A5}
dADP1 = seq {P1M P1 A5}
dADP2 = seq {P2M P1 A5}
dATP1 = seq {P1M P1 P1 A5}
dATP2 = seq {P2M P1 P1 A5}
dAQP1 = seq {P1M P1 P1 P1 A5}
dAQP2 = seq {P2M P1 P1 P1 A5}

AMP1 = seq {P1M B5}
AMP2 = seq {P2M B5}
ADP1 = seq {P1M P1 B5}
ADP2 = seq {P2M P1 B5}
ATP1 = seq {P1M P1 P1 B5}
ATP2 = seq {P2M P1 P1 B5}
AQP1 = seq {P1M P1 P1 P1 B5}
AQP2 = seq {P2M P1 P1 P1 B5}


regards, Francois

> ________________________________________
> From: FyD []
> Sent: Tuesday, July 08, 2014 5:20 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] ATP and Mg2+ parameters
> Dear Valentina,
>> I would like to run a MD for a protein kinase in complex with ATP
>> and a Mg2+ ion.
>> Do you know if parameters for ATP and Mg2+ already exist?
>> Or should I use antechamber?
> ATP, ADP, AMP are in R.E.DD.B.
> see
> regards, Francois

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Received on Tue Jul 15 2014 - 04:30:02 PDT
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