AMBER Archive (2008)

Subject: AMBER: xleap fails to savemol2

• Next message: Ilyas Yildirim: "RE: AMBER: to understand how frcmod.ff99SB works"
• Previous message: Robert Duke: "Re: AMBER: pmemd iwrap trouble"
• In reply to: Thomas Cheatham III: "Re: AMBER: pmemd iwrap trouble"
• Next in thread: FyD: "Re: AMBER: xleap fails to savemol2"
• Reply: FyD: "Re: AMBER: xleap fails to savemol2"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Hi,

I am trying to save a mol2 file using xleap (AMBER 10)

i have a mol2 file, i can read it just fine with xleap and i can also
convert it to *.prmtop and *.inpcrd. However i cannot savemol2.

my script:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams mysioforce.frcmod
sur = loadmol2 "newsurface.mol2"
check sur
saveamberparm surfacealone.prmtop surfacealone.inpcrd
savepdb sur surface.pdb
savemol2 sur surface0.mol2 0
savemol2 sur surface1.mol2 1
solvatebox sur TIP3PBOX 8.0
saveamberparm surfacesolvent.prmtop surfacesolvent.inpcrd
edit sur

i attached mysioforce.frcmod and newsurface.mol2
savepdb fails and savemol2 (0 and 1) causes xleap to crash.

Any suggestions?,
Taufik

• text/plain attachment: modified force

• chemical/x-mol2 attachment: original mol2 file

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu

• Next message: Ilyas Yildirim: "RE: AMBER: to understand how frcmod.ff99SB works"
• Previous message: Robert Duke: "Re: AMBER: pmemd iwrap trouble"
• In reply to: Thomas Cheatham III: "Re: AMBER: pmemd iwrap trouble"
• Next in thread: FyD: "Re: AMBER: xleap fails to savemol2"
• Reply: FyD: "Re: AMBER: xleap fails to savemol2"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]