Re: [AMBER] RESP: optimized charges not reasonable

From: Ignacio Faustino Plo <ignacio.faustino.irbbarcelona.org>
Date: Tue, 29 Mar 2011 12:46:12 +0200

Thanks Francois. I forgot to attach the output file. In any case I will check the RED procedure and server facilities.

Thaks

 in advance.

Best,
Ignacio.

On mar 29, 2011, at 10:36 a.m., FyD wrote:

> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Mar 29 2011 - 04:00:02 PDT
Custom Search