Dear Valentina,
> 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
This is the whole molecule approach: this approach is generally
applied to small molecules, which are not multiply charged, and/or
with well identified conformation(s)...
This is why in your case I suggested you the building block approach
(instead of that whole molecule approach):
at
http://q4md-forcefieldtools.org/REDDB/projects/F-90/ it is written:
"The building block approach presents the following advantages over
the whole molecule approach: (i) the cpu time required for geometry
optimization and molecular electrostatic potential (MEP) computation
is drastically decreased, (ii) the optimized geometry of the
conformation(s) of each building block is fully defined and
controlled, (iii) conformations not suited for charge derivation,
presenting non-bonded interactions only observed in gas phase geometry
optimization are discarded, (iv) cofactors and their analogs are
simultaneously involved in a single and highly homogenous approach,
and finally (v) by generating averaged charge values for connecting
groups, additional and highly compatible charge derivation procedures
can be performed for an infinity of new cofactor analogs constituting
"add-ons" to the present R.E.DD.B. project."
> is correct or if I do not had to take into account. Same question for
> the provided prep files.
Concercing force field library file formats:
i.e. mol2/mol3 vs prep/off please read:
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
and then
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
the mol3 file format has been specially designed for molecular
fragments and for the building block approach... (the prep file format
is quite old; then came out the off, mol2 and mol3 ones)
regards, Francois
> 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?
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Received on Thu May 29 2014 - 00:30:02 PDT
