Hi,
You could look in R.E.DD.B. and in the W-46 project:
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/
See
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/tripos7.mol2
&
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/script1.ff
tleap -f script1.ff
you can also look at the demo of R.E.D. Server Dev./R.E.D. Python:
http://q4md-forcefieldtools.org/REDS-Development/
http://q4md-forcefieldtools.org/REDS-Development/RED-Server-demo1.php
http://q4md-forcefieldtools.org/REDS-Development/popup/poptestcase.php
here is the input used by the demo:
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Mol-7.pdb
After running the demo a graphical web interface is generated to parse
R.E.D. python output and display the generated force field for the 10
input molecules (FF libraries in the mol3 file format, force field
parameters and leap script)
I hope this helps
regards,
Francois
> 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:
> 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
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Received on Wed Mar 05 2014 - 23:00:02 PST
