AMBER Archive (2007)

Subject: AMBER: antechamber --> sander problem

From: Yamada, Takahiro (Takahiro.Yamada_at_udri.udayton.edu)
Date: Fri Nov 16 2007 - 14:18:18 CST

Dear AMBER users,

 

I have a special system which is butadiene-acrylonitrile-butadiene
monomer solvated with TIP3PBOX. I exactly followed Tutorial B4 (sustiva
solvated with TIP3PBOX) to make prmtop and inpcrd. Then I tried to run
sander, but I failed to run. The end on output file said "Error:
ifbox=2 in prmtop but angles are not correct." Attached are prmtop,
inpcrd, out, and 2 pdb files (one for original
butadiene-acrylonitrile-butadiene monomer, and one for monomer solvated
with water which I recreated using ambpdb command). I appreciate if
anyone could tell me what is wrong. I am new AMBER user and trying to
apply AMBER code to model polymer - organic solvent interaction. I
created this system as a 1st step to examine if AMBER can be used for my
research.

 

Thank you.

 

   

 

Takahiro Yamada, Ph.D.

Research Chemist

Environmental Engineering Group

University of Dayton Research Institute

takahiro.yamada_at_udri.udayton.edu

 



  • application/octet-stream attachment: bnb3.out

  • application/octet-stream attachment: bnb3.PDB


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu