Dear Ignacio,
This is difficult to help without the RESP output(s)...
It looks like the phosphorus atom is 'with' the nucleoside in a single
molecule.
See Cieplak et al. J.Comput.Chem. 1995,16,1357-1377 for deriving
charges for nucleotide fragments for the Amber force field.
You could use R.E.D. or R.E.D. Server to derive RESP charges for your
modified nucleotide. RESP inputs are automatically generated.
See
http://q4md-forcefieldtools.org/
You can also find tutorials . q4md-forcefieldtools.org for your problem.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#18
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
You can find examples of modified nucleotides in R.E.DD.B. as well.
regards, Francois
Quoting Ignacio Faustino Plo <ignacio.faustino.irbbarcelona.org>:
> Dear member list,
>
> I am running some calculations for getting the corresponding RESP
> charges for a modified nucleotide. After optimization and ESP
> calculation, RESP is giving huge atomic charges for some of the
> atoms (numbers like 3 or 4 are unreasonable). Could you give some
> advice on this issue?
>
> Here is the input file I am using:
>
> RESP calculation
> &cntrl
> ihfree=1,
> qwt=0.0005,
> iqopt=2
> /
> 1.0
>
> -1 35
> 7 0
> 6 0
> 6 0
> 6 0
> 7 0
> 6 0
> 6 0
> 6 0
> 8 0
> 7 0
> 7 0
> 1 0
> 1 0
> 1 0
> 8 0
> 6 0
> 6 0
> 6 0
> 6 0
> 1 0
> 1 0
> 1 0
> 1 0
> 1 0
> 6 0
> 8 0
> 1 0
> 1 0
> 1 0
> 8 0
> 1 0
> 1 0
> 15 0
> 8 0
> 8 0
> EOF
>
> Thanks in advance.
>
> Ignacio
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Received on Tue Mar 29 2011 - 02:00:02 PDT
