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
>>
>
>
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Received on Sun May 29 2016 - 05:30:02 PDT
