Dear Amber users,
I am following the antechamber tutorial 4b for creating topology and
co-ordinate
files for a complex. After creating .prmtop and .inpcrd file for the
organic molecule using R.E.D server created .mol2 file, I tried to complex
the organic molecule with the protein. But, it was showing the error that
the molecule is an unknown residue and atoms were not in its residue
template. An archive file of the operation is attached with the mail.
The commands typed are :
1. parmchk -i sam.mol2 -f mol2 -o sam.frcmod
2. tleap -f leaprc.ff12SB
3. source leaprc.gaff
4. dem = loadmol2 sam.mol2
5. check dem
6. loadamberparams sam.frcmod
7. saveoff dem sam.lib
8. saveamberparm dem sam.prmtop sam.inpcrd
9. loadamberparams sam.frcmod
10.loadoff sam.lib
11.com = loadpdb hArsM.pdb
12.saveamberparm com hArsM.prmtop hArsM.inpcrd
Please suggest what may be the problem causing these errors and how to
counter them.
Thanking you,
Swithin Hanosh
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Received on Mon Apr 06 2015 - 22:30:02 PDT
