Hi Francois,
thanks for your reply, I will try to generate the files that I need with
the RED server.
Btw, I am still wondering if the procedure described here
http://ambermd.org/antechamber/dna.html
is correct or if I do not had to take into account. Same question for
the provided prep files.
Regards,
Valentina
Il 05/05/2014 07:19, FyD ha scritto:
> Dear Valentina,
>
> You could use R.E.D. Server Dev. at
> http://q4md-forcefieldtools.org/REDServer-Development/
>
> to develop force field libraries for the non-protonated and protonated
> phosphate groups.
>
> In the F-90 REDDB project you can find examples of non-protonated and
> protonated phosphate groups as examples:
> http://q4md-forcefieldtools.org/REDDB/projects/F-90/
> http://q4md-forcefieldtools.org/REDDB/projects/F-91/
>
> R-OH Me-OPO3(2-) ---> R-OPO3(2-)
> Me-OPO3H(-) R-OPO3H(-)
>
> You use two inter-mcc between the OH group of the 'R-OH' building
> block and the Me group of 'Me-OPO3(2-)' and 'Me-OPO3H(-)'
>
> R.E.D. Server Dev. performs charge dervation, force field library
> building and force field parameter generation; key points here are
> atom typing for molecular fragments and fragment fusion between the 3
> elementary building blocks.
>
> force field parameters are in the frcmod.* files
>
> all should be done automatically.
>
> See the documentation:
> http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>
> regards, Francois
>
>
>> I have a DNA G-quadruplex with total net charge of -17. I would like to
>> protonate some phosphate groups of the guanines to reach the net charge
>> of -5 (in according with my experimental mass data), and then run a MD
>> simulation in gas phase.
>>
>> I have found here http://ambermd.org/antechamber/dna.html the prep file
>> for the protonated guanine and I have generated the frcmod file with
>> parmchk2. After that I have modified my pdb file to replace the residue
>> names of the guanines and then I have used leap to generate prmtop and
>> inpcrd files (leap.log attached).
>>
>> Basically I have obtained the net charge of -5 that I wanted, but also
>> some "warnings" and improper torsions that I do not understand to what
>> they are due. prmtop and inpcrd seem fine but if I try to minimize the
>> structure, I end up with improper conformations of the protonated
>> guanines (NH2 of the base not in the plane), and then totally weird
>> conformations during the equilibration that ends with the unfolding of
>> the structure (restart file attached).
>>
>> I guess that everything is related to what I have done in leap.
>>
>> Please, could you help me to understand what is going wrong?
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
----
5x1000 AI GIOVANI RICERCATORI
DELL'UNIVERSITÀ DI NAPOLI
Codice Fiscale: 00876220633
www.unina.it/Vademecum5permille
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 28 2014 - 09:30:02 PDT
