Dear
All,
I
tried to prepare a structure to get the prmtop and inpcrd input files
for ff03ua force field. And I did all the operations in below. But
after I got the frcmod file , I realized that there are some AA force
field parameters in it. So I thougt that I didn't / couldn't generate
a UA prepin file for my MD simulations. I attached the prep and
frcmod files to the mail. What should I do to generate UA prepin and
frcmod files for n-alkanes and use these file for Amber ff03ua ?
Thanks
in advance
Sincerely
1antechamber
-i n-octane.pdb -fi pdb -o octane_gin.gjf -fo gcrt
2
Run the gaussian ( #B3LYP/cc-pvTZ SCF=tight Test Pop=MK iop(6/33=2)
iop(6/42=6) opt )
3
antechamber -i octane_gin.out -fi gout
-o octane.prep -fo prepi -nc 0 -c resp -at amber -rn
OAS
4
parmchk -i octane.prep -f prepi -o octane.frcmod
5 antechamber
-i octane.prep -fi prepi -o octane.ff03ua.pdb -fo pdb
6 use
packmol with octane.ff03ua.pdb for getting 10 molecule ( added TER
cards ) octane10.packmol.pdb file
7 xleap
-s -f leaprc.ff03ua
8 loadAmberPrep
octane.prep
9 loadamberparams
octane.frcmod
10 check
OAS
11
octane = loadpdb octane10.packmol.pdb
12 check
octane ( unit is OK )
13
saveamberparams octane octane10.prmtop octane10.inpcrd
14
Quit
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Received on Fri Dec 26 2008 - 01:15:40 PST
