*Summary*
*(The script runs fine if I manually input the names but obviously would
rather not do that each time. *
*1. I cannot get my variables to transfer across from the bash line into
tleap*
*2. I cant get script 3 to run after doing the tleap caculation *
So I want to run some files through tleap
I generate the input using antechamber then parmchk
Then I open up a new script in tleap (But want the variables $1 etc. to
come with it)
I then try to open a 3rd script but it doesnt let me
To run I type ./Script1 $1 (Where $1 is a name like 2XHX)
Script 1
antechamber/parmchk commands (just not typing out in full to save space)
NAME=$1
export NAME
tleap -f Script 2
Script 2
#!/bin/bash
source leaprc.gaff
source leaprc.ff14SB
source leaprc.tip3p
gaff=loadamberparams gaff.dat
LIG=loadmol2 $NAMEL.mol2
loadamberparams $NAMEL.frcmod
saveoff LIG $NAMEL.lib
complex=loadpdb $NAME.pdb
solvatebox complex TIP3PBOX 8.0
loadamberparams frcmod.ionsjc_tip3p
addIons2 complex Na+ 0
addIons2 complex Cl- 0
saveamberparm complex $NAME.prmtop $NAME.crd
quit
export NAME
export GPU
./Script 3
Script 3 is a set of bashline commands to run CUDA
*So to summaries*
*(The script runs fine if I manually input the names but obviously would
rather not do that each time)*
*1. I cannot get my variables to transfer across from the bash line into
tleap*
*2. I cant get script 3 to run after doing the tleap caculations.*
Just a side note I am aware that I am running some older versions of things
and I am trying to get that updated but it is going to take some time.
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Received on Mon Aug 20 2018 - 03:00:03 PDT
