I am trying to generate topology for trytophan molecule which has been modified slightly.
The PDB file for this is attached.
I have used antecmber to generate prepin file using the comamnd as below:
antechamber -i tryptofanC0.pdb -fi pdb -o tryptofanC0.prepin -fo prepi -c bcc -s 2
This generated charges using (AM1-BCC).
Next I generated frcmod file using command parmchk:
parmchk -i tryptofanC0.prepin -f prepi -o tryptofanC0.frcmod
Then, I loaded the prepin, frcmod and pdb files in tleap together with leaprc files using command as below
tleap -f moleculeNew.leap where file moleculeNew.leap contains lines as blow:
source leaprc.lipid11
source leaprc.ff12SB
source leaprc.GLYCAM_06j_12SB
source leaprc.gaff
loadamberprep tryptofanC0.prepin
loadamberparams tryptofanC0.frcmod
trpC0 = loadpdb tryptofanC0.pdb
charge trpC0
check trpC0
saveamberparm trpC0 try2fanC0.top try2fanC0.crd
quit
At the point it finishes I get some messages related to improper torsion angles. The message is as below:
=======================================================================================
vijay.glycosim:~/Simulation-Folder-Feb2013/other-systems/project-Osama/03-model-bilayers/1-preparation-system/MODEL-both/TrytophanC0$ tleap -f vj-amberInput-file.leap
-I: Adding /usr/local/apps/amber12/dat/leap/prep to search path.
-I: Adding /usr/local/apps/amber12/dat/leap/lib to search path.
-I: Adding /usr/local/apps/amber12/dat/leap/parm to search path.
-I: Adding /usr/local/apps/amber12/dat/leap/cmd to search path.
-f: Source vj-amberInput-file.leap.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./vj-amberInput-file.leap
----- Source: /usr/local/apps/amber12/dat/leap/cmd/leaprc.ff12SB
----- Source of /usr/local/apps/amber12/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: /usr/local/apps/amber12/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/local/apps/amber12/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /usr/local/apps/amber12/dat/leap/lib/amino12.lib
Loading library: /usr/local/apps/amber12/dat/leap/lib/aminoct12.lib
Loading library: /usr/local/apps/amber12/dat/leap/lib/aminont12.lib
Loading library: /usr/local/apps/amber12/dat/leap/lib/nucleic12.lib
Loading library: /usr/local/apps/amber12/dat/leap/lib/ions08.lib
Loading library: /usr/local/apps/amber12/dat/leap/lib/solvents.lib
Could not open file leaprc.GLYCAM_06j_12SB: not found
----- Source: /usr/local/apps/amber12/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/apps/amber12/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/apps/amber12/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.5, January 2013)
Loading Prep file: ./tryptofanC0.prepin
Loading parameters: ./tryptofanC0.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading PDB file: ./tryptofanC0.pdb
total atoms in file: 27
Total unperturbed charge: 0.000000
Total perturbed charge: 0.000000
Checking 'trpC0'....
Checking parameters for unit 'trpC0'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<TR0 1>: CA OXT C O
<TR0 1>: CB CD2 CG CD1
<TR0 1>: CG HD1 CD1 NE1
<TR0 1>: CE2 CD1 NE1 HE1
<TR0 1>: CD2 CZ2 CE2 NE1
<TR0 1>: CE2 CE3 CD2 CG
<TR0 1>: CD2 CZ3 CE3 HE3
<TR0 1>: CE3 CH2 CZ3 HZ3
<TR0 1>: CZ3 CZ2 CH2 HH2
<TR0 1>: CE2 CH2 CZ2 HZ2
total 10 improper torsions applied
10 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
Quit
vijay.glycosim:~/Simulation-Folder-Feb2013/other-systems/project-Osama/03-model-bilayers/1-preparation-system/MODEL-both/TrytophanC0$
=========================================================================================
My questions are:
1) Is there any error in the making of topology and incrd files?
2) Is my charges are correct?
3) Later I want to mix this molecule into glycolipid. So do I need to incorporate the GLYCAM force fields in the making of topology and incrd of this molecule?
4) Can anyone give brief idea the importance of "improper torsion angles"?
Appreciate one can help.
Many thanks in advance.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Wed Mar 19 2014 - 07:00:03 PDT
