Dear all
I am new to amber and I am doing tutorial 4 with amber9. I followed all the steps as mentioned in the tutorial.
I when I put the command $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_AC.AC0 ANTECHAMBER_AC.A divcon.in divcon.out ANTECHAMBER_AM1BCC_PRE.AC ANTECHAMBER_AM1BCC.AC ATOMTYPE.INF sustiva.pdb sustiva.mol2
There is file no file written my directory with the following names
divicon.pdb mopac.in mopac.out mopac.pdb
Ignoring this I when with the remaining steps in the tutorial and I used the parmchk utility and then put the command
$AMBERHOME/exe/parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
A file called sustiva.frcmode was produced. I opened xleap loaded it with sustiva.mol2checked SUS and opened and closed the edit widow . I put the commanded
loadamberparams sustiva.frcmod
to tell the xleap the parameter for missing angle types
but when check out the SUS unit again there is still a missing angle parameter and I could not get the prmtop and inpcrd files
Is it because I am using amber9? Can anyone tell me what do?
Thank you
Workalemahu
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Received on Thu May 28 2009 - 01:10:11 PDT
