Hello amber users
I am using amber 10 to simulate small molecules (modified a little as
compared to original pdb structure). First I used antechamber to fit ligand
parameters and then I used tleap to generate library in this way -
~/src/Xtruct/trunk/amber_10_install/bin/antechamber -i DXQ-11_h.pdb -fi pdb
-o DXQ-11.mol2 -fo mol2 -c bcc -s 2 -j 5 -nc +2
parmchk -i DXQ-11.mol2 -f mol2 -o DXQ-11.frcmod
Then -
source leaprc.ff99SB
source leaprc.gaff
DXQ = loadmol2 DXQ-11.mol2
loadamberparams DXQ-11.frcmod
check DXQ
saveoff DXQ DXQ-11.lib
saveamberparm DXQ DXQ-11.prmtop DXQ-11.inpcrd
quit
After this when I wish to create prmtop and inpcrd files for complex -
source leaprc.ff99SB
source leaprc.gaff
loadoff DXQ-11.lib
loadamberparams DXQ-11.frcmod
complex=loadpdb complex.pdb
receptor=loadpdb receptor.pdb
ligand=loadpdb DXQ-11.pdb
saveamberparm complex complex.prmtop complex.inpcrd
saveamberparm receptor receptor.prmtop receptor.inpcrd
saveamberparm ligand ligand.prmtop ligand.inpcrd
addions complex Na+ 0
solvatebox complex TIP3PBOX 8.0
saveamberparm complex solvated_complex.prmtop solvated_complex.inpcrd
savepdb complex solvated_complex.pdb
quit
It gives error messages -
FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAB 2> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAD 3> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAE 4> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAF 5> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAG 6> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAH 7> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAI 8> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAJ 9> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAK 10> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAL 11> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAN 12> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAO 13> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAP 14> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAQ 15> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAR 16> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAS 17> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAY 18> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CAZ 19> does not have a type.
FATAL: Atom .R<LIG 1184>.A<NAV 20> does not have a type.
FATAL: Atom .R<LIG 1184>.A<OAW 21> does not have a type.
FATAL: Atom .R<LIG 1184>.A<OAX 22> does not have a type.
FATAL: Atom .R<LIG 1184>.A<CBE 23> does not have a type.
FATAL: Atom .R<LIG 1184>.A<NBF 24> does not have a type.
FATAL: Atom .R<LIG 1184>.A<NBG 25> does not have a type.
FATAL: Atom .R<LIG 1184>.A<NBH 26> does not have a type.
FATAL: Atom .R<LIG 1184>.A<NBI 27> does not have a type.
FATAL: Atom .R<LIG 1184>.A<N1 28> does not have a type.
FATAL: Atom .R<LIG 1184>.A<C2 29> does not have a type.
FATAL: Atom .R<LIG 1184>.A<N3 30> does not have a type.
FATAL: Atom .R<LIG 1184>.A<C4 31> does not have a type.
FATAL: Atom .R<LIG 1184>.A<C5 32> does not have a type.
FATAL: Atom .R<LIG 1184>.A<C6 33> does not have a type.
Failed to generate parameters
Could you tell what the problem is.
Thank you
Regards,
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Received on Wed Jul 21 2010 - 05:30:04 PDT
