This is not a trivial problem. Parameters for ATP, GTP are available
(
http://sites.pharmacy.manchester.ac.uk/bryce/amber/ ... there may be
others available as well).. and could be a good starting point ....
However, you need to double check which version of the force field for
DNA you'd like to use ... It may be that you need to adapt the backbone
parameters to match the newest ff modifications for DNA
You may also need a new charge derivation procedure if you modify the
backbone dihedrals...For this you could check this:
http://upjv.q4md-forcefieldtools.org/RED/
Alternatively you may ask the authors of the newest ff modifications for
DNA whether they do not have parameters for such nucleotides that are
not published yet ...
Hope this helps
Vlad
On 05/29/2016 02:23 PM, M. Reza Ganjalikhany wrote:
> Dear Amber experts,
> I have already checked all the previous emails in the mailing list to find
> a standard procedure to safely parameterize three-phosphate-nucleotide at
> 5' end of a DNA molecule and all methods have been tested but non of them
> were helpful. There is a helpful email which is archived from 2006 but all
> the links were inactive and not operational.
> http://structbio.vanderbilt.edu/archives/amber-archive/2006/2341.php
>
> I would be grateful is any body could help me with this problem.
>
> On Fri, May 27, 2016 at 2:02 PM, M. Reza Ganjalikhany <
> ganjalikhany.gmail.com> wrote:
>
>> I used same names for mol2, Lib and PDB files but think that Leap does
>> not use my library.
>>
>> On Fri, May 27, 2016 at 12:55 PM, Vlad Cojocaru <
>> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>
>>> The atom and residue names in your Leap library (mol2 or off library,
>>> don't know what you used) should exactly match the corresponding names
>>> in your complete PDB file ...otherwise it will not work because leap
>>> only knows what is in its template libraries ... So, playing with names
>>> will not help you, you have to match the names 100% to the Leap library
>>> ...
>>>
>>> Vlad
>>>
>>>
>>> On 05/27/2016 10:11 AM, M. Reza Ganjalikhany wrote:
>>>> Dear Amber Users,
>>>>
>>>> I want to simulate a DNA structure (DNAzyme) with a nick ( 5'
>>>> three-phosphate) inside the structure. I introduced a nick and add
>>>> three-phosphate to the Guanine, then I followed the standard procedure
>>>> with *antechamber
>>>> *to generate *library *and *frcmod * for this three-phosphate Guanine.
>>>> These file have been successfully generated and then I used these files
>>>> for generating parameter topology and input coordination for the whole
>>>> DNAzyme structure.
>>>> Unfortunately I got the " atoms not in residue templates" error from the
>>>> xleap for the P and O atoms.
>>>> I tried different name for phosphate and oxygen as below:
>>>> Alpha-beta-gamma phosphate
>>>> PA
>>>> O1A
>>>> O2A
>>>> PB
>>>> O1B
>>>> O2B
>>>> PG
>>>> O1G
>>>> O2G
>>>> O3G
>>>>
>>>> and also use plain P or O
>>>> P
>>>> OP1
>>>> OP2
>>>> ..
>>>> .
>>>>
>>>> but non of them helped me to solve the problem.
>>>> I used Hyperchem to add three-phosphate to Guanine residue, so I edited
>>>> these name according to standard names.
>>>> Is there any standard method for nomenclature of Phosphate and Oxygen
>>>> groups?
>>>> Should I use Chimera to generate there files or is there any procedure
>>> to
>>>> solve these phosphate-type-errors?
>>>>
>>>> Any help would be greatly appreciated.
>>>>
>>>> Regards,
>>>> M. Reza
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> --
>>> Dr. Vlad Cojocaru
>>> Computational Structural Biology Laboratory
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
>>> _______________________________________________
>>> 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
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Sun May 29 2016 - 06:00:04 PDT
