[AMBER] about atom type

From: Navanath Kumbhar <nmkumbhar.gmail.com>
Date: Tue, 15 Jun 2010 10:55:29 +0530

Dear Sir,

i had set atom type for modified nucleosides as like that of .frcmod file
downloaded from Amber web site.It was defined well for all atoms except N1,
it gives error as

>set mod.1.N1 type N*
set: improper Number of arguments!
usage :set <container > <parameter > <object>
or set default parameter value

when i set N1 atom by selecting it from edit menu and change type as N*
and saveOff mod mod.lib
when i again try to open my mod.pdb file it

source leaprc.ff99SB
loadOff mod.lib
mod=loadpdb mod.pdb
edit mod

it created again new atom name for every atoms
it shows molecule without bond (just like when we open the pdb file)

whether my procedure is wrong?

Please give any suggestion to solve this problem.

Thanks and great regards
Navanath Kumbhar
AMBER mailing list
Received on Mon Jun 14 2010 - 22:30:06 PDT
Custom Search