Re: [AMBER] problem to generate parameters files from NMR solved DNA structure

From: Ananya Paul <a3diisc.gmail.com>
Date: Thu, 11 Mar 2010 19:10:54 +0530

Dear Sir,
I am using Amber 9 Tools and following leap commands for generating the
parameter files.

source leaprc.gaff
loadamberprep RES.prepin
loadamberparams RES.frcmod
dlc=loadpdb dlc.pdb
addions dlc K+ 0
solvatebox dlc TIP3PBOX 10.0
saveamberparm dlc dlc.prmtop dlc.inpcrd
quit

and the leaprc file is

source /soft/amber9/dat/leap/cmd/leaprc.ff99

 2HY9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-O8

I am attaching the leap.log file.
Thank you
Ananya




On Thu, Mar 11, 2010 at 6:16 PM, case <case.biomaps.rutgers.edu> wrote:

> On Thu, Mar 11, 2010, Ananya Paul wrote:
>
> > When I am trying to generate parameter file (.pratop, .inpcrd) taking
> NMR
> > solved structure 2HY9, it is showing following error
> > FATAL: Atom .R<DT 1>.A<H5' 33> does not have a type.
> > FATAL: Atom .R<DT 1>.A<H5'' 34> does not have a type.
>
> We need to know which leaprc file you used and which version of AmberTools
> you are using. It's probably best to report all the leap commands that
> were
> used. It looks like you have a current (version 3) pdb file, and
> up-to-date
> Amber files should handle this fine.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Ananya Paul
Senior Research Fellow
Dept. of Organic Chemistry
Indian Institute of Science, Bangalore



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Thu Mar 11 2010 - 06:00:03 PST
Custom Search