Hi,
I am adding two small molecules in a library, but 8 atoms are not in
residue templates when I load combine pdb. I checked my library file, atoms
symbol are same there. I parametrized using antechamber and parmchk and
combine pdbs by packmol. Here is my code
antechamber -i mol1.pdb -fi pdb -o mol1.mol2 -fo mol2 -c bcc -nc 1
antechamber -i mol2pdb -fi pdb -o mol2.mol2 -fo mol2 -c bcc -nc 1
parmchk -i mol1.mol2 -f mol2 -o mol1.frcmod -a Y -w Y
parmchk -i mol2.mol2 -f mol2 -o mol2.frcmod -a Y -w Y
source oldff/leaprc.ff99SB
source leaprc.gaff
loadamberparams mol1.frcmod
loadamberparams mol2.frcmod
UNK=loadmol2 mol1.mol2
saveoff UNK molecule.lib
LIG= loadmol2 mol2.mol2
saveoff LIG molecule.lib
loadoff molecule.lib
> pdb=loadpdb solvprotein.pdb
Loading PDB file: ./solvprotein.pdb
-- residue 1: duplicate [ C] atoms (total 2)
-- residue 1: duplicate [ C1] atoms (total 2)
-- residue 1: duplicate [ C2] atoms (total 2)
-- residue 1: duplicate [ C3] atoms (total 2)
-- residue 1: duplicate [ H] atoms (total 2)
-- residue 1: duplicate [ H1] atoms (total 2)
-- residue 1: duplicate [ H10] atoms (total 2)
-- residue 1: duplicate [ H11] atoms (total 2)
-- residue 1: duplicate [ H2] atoms (total 2)
-- residue 1: duplicate [ H3] atoms (total 2)
-- residue 1: duplicate [ H4] atoms (total 2)
-- residue 1: duplicate [ H5] atoms (total 2)
-- residue 1: duplicate [ H6] atoms (total 2)
-- residue 1: duplicate [ H7] atoms (total 2)
-- residue 1: duplicate [ H8] atoms (total 2)
-- residue 1: duplicate [ H9] atoms (total 2)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Created a new atom named: O within residue: .R<UNK 1>
Created a new atom named: O1 within residue: .R<UNK 1>
Created a new atom named: O2 within residue: .R<UNK 1>
Created a new atom named: O3 within residue: .R<UNK 1>
Created a new atom named: O4 within residue: .R<UNK 1>
Created a new atom named: oh within residue: .R<UNK 1>
Created a new atom named: P within residue: .R<UNK 1>
Created a new atom named: Si within residue: .R<UNK 1>
total atoms in file: 86
The file contained 8 atoms not in residue templates.
I read previous answer but I can't figure out.
Best
Amen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 09 2019 - 11:30:02 PDT
