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From: kamlesh sahu <kamleshsemail.gmail.com>

Date: Wed, 21 Jul 2010 21:11:34 +0900

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,

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Jul 21 2010 - 05:30:04 PDT

Date: Wed, 21 Jul 2010 21:11:34 +0900

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,

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Jul 21 2010 - 05:30:04 PDT

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