Re: [AMBER] Simulation of DNA structure with a three-phosphate at 5'

From: Vlad Cojocaru <>
Date: Fri, 27 May 2016 10:25:30 +0200

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 ...


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

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]
AMBER mailing list
Received on Fri May 27 2016 - 01:30:05 PDT
Custom Search