AMBER Archive (2008)

Subject: AMBER: a question about ff03ua

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Thu Dec 25 2008 - 08:06:33 CST

        
        
        
        
        

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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