Re: [AMBER] difficulties in generate .prmtop and .inpcrd file

From: MarcZhang <progress0935zhang.gmail.com>
Date: Thu, 15 Oct 2015 22:07:10 +0200

Dear Emilio Lence

 

Thanks a lot for your reply

 

Here is my instructions to tleap for ligand parameter generation:

 

set default PBradii mbondi2

source leaprc.ff99SB

source leaprc.gaff

BP1=loadmol2 BPH-TTR_Ligand1_resp.mol2

loadamberparams BPH-TTR_Ligand1_resp.frcmod

loadamberprep BPH-TTR_Ligand1_resp.prep

check BP1

saveoff BP1 BP1.lib

saveamberparm BP1 BPH-TTR_BP1_resp_nW.prmtop BPH-TTR_BP1_resp_nW.inpcrd

quit

 

Here is the instructions to tleap for complex parameter generation:

 

set default PBradii mbondi2

source leaprc.ff99SB

source leaprc.gaff

loadamberparams frcmod.ionsjc_tip3p

loadamberparams BPH-TTR_Ligand1_resp.frcmod

loadamberprep BPH-TTR_Ligand1_resp.prep

loadoff BP1.lib

check

Complex=loadpdb BPH-TTR_Complex.pdb

saveamberparm Complex BPH-TTR_Complex_nW.prmtop BPH-TTR_Complex_nW.inpcrd

savepdb Complex BPH-TTR_Complex_nW.pdb

solvateoct Complex TIP3PBOX 10.0

charge Complex

addions Complex Na+ 0

addions Complex Cl- 0

charge Complex

check Complex

saveamberparm Complex BPH-TTR_Complex_Solvated.prmtop
BPH-TTR_Complex_Solvated.inpcrd

savepdb Complex BPH-TTR_Complex_Solvated.pdb

quit

 

Can you figure out where the issue it? Please inform me if you require more
information.

 

Thanks very much!

 

Cheers

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Received on Thu Oct 15 2015 - 13:30:04 PDT
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