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
Received on Fri May 27 2016 - 03:00:02 PDT
