Hi al ,
I have use xleap to produce a small molecular of 'ch3cn',and I want to use
antechamber to produce the prmtop file. I don't know how to correct it. Can
you help me to resolve it ? Thank you very much
The PDB file:4.pdb
ATOM 1 C1 LIG 1 -0.000 -0.000 -0.000 1.00 0.00
ATOM 2 H1 LIG 1 1.000 0.000 0.000 1.00 0.00
ATOM 3 H2 LIG 1 -0.334 0.943 0.000 1.00 0.00
ATOM 4 H3 LIG 1 -0.334 -0.472 0.816 1.00 0.00
ATOM 5 C2 LIG 1 -0.434 -0.614 -1.061 1.00 0.00
ATOM 6 N1 LIG 1 -0.801 -1.134 -1.958 1.00 0.00
TER
Command:
antechamber -i 4.pdb -fi pdb -o 4.mol2 -fo mol2 -j 5 -c bcc
parmchk -i 4.mol2 -f mol2 -o 4.frcmod
Leapin£º
source leaprc.ff99SB
LIG = loadmol2 4.mol2
check LIG
loadamberparams 4.frcmod
saveoff LIG 4.lib
saveamberparm LIG 4.prmtop 4.inpcrd
The tleap result:-I: Adding /apps/amber12/dat/leap/prep to search path.
-I: Adding /apps/amber12/dat/leap/lib to search path.
-I: Adding /apps/amber12/dat/leap/parm to search path.
-I: Adding /apps/amber12/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source x.
Welcome to LEaP!
Sourcing: ./x
----- Source: /apps/amber12/dat/leap/cmd/leaprc.ff99SB
----- Source of /apps/amber12/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /apps/amber12/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /apps/amber12/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /apps/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /apps/amber12/dat/leap/lib/all_amino94.lib
Loading library: /apps/amber12/dat/leap/lib/all_aminoct94.lib
Loading library: /apps/amber12/dat/leap/lib/all_aminont94.lib
Loading library: /apps/amber12/dat/leap/lib/ions94.lib
Loading library: /apps/amber12/dat/leap/lib/solvents.lib
Loading Mol2 file: ./4.mol2
Reading MOLECULE named LIG
Checking 'LIG'....
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Could not find bond parameter for: c3 - hc
Could not find bond parameter for: c3 - hc
Could not find bond parameter for: c3 - hc
Could not find bond parameter for: c3 - c1
Could not find bond parameter for: c1 - n1
Checking for angle parameters.
Could not find angle parameter: c3 - c1 - n1
Could not find angle parameter: hc - c3 - hc
Could not find angle parameter: hc - c3 - hc
Could not find angle parameter: hc - c3 - c1
Could not find angle parameter: hc - c3 - hc
Could not find angle parameter: hc - c3 - c1
Could not find angle parameter: hc - c3 - c1
There are missing parameters.
Unit is OK.
Loading parameters: ./4.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<LIG 1>.A<C1 1> Could not find vdW (or other) parameters for
type: c3
For atom: .R<LIG 1>.A<H1 2> Could not find vdW (or other) parameters for
type: hc
For atom: .R<LIG 1>.A<H2 3> Could not find vdW (or other) parameters for
type: hc
For atom: .R<LIG 1>.A<H3 4> Could not find vdW (or other) parameters for
type: hc
For atom: .R<LIG 1>.A<C2 5> Could not find vdW (or other) parameters for
type: c1
For atom: .R<LIG 1>.A<N1 6> Could not find vdW (or other) parameters for
type: n1
Parameter file was not saved.
.
The second question:
When I use gv and antechamber to produce the molecular of ¡®ch3cn' ,it
can't be recognized by autodock.Is there anything special of 'ch3cn'? Thank
you
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 05 2014 - 00:30:04 PST
