Hi,
In the last few years I have used GROMAC in my research. Recently I moved
to work with amber (amber12).
Currently, I am trying to study cyclic peptides, in which the backbone
amino group of the first residue has a peptide-bond with the carboxyl
backbone group of the last residue. My question is how to do this in tleap.
I tried to use 'crosslink' and 'bond' but the FF missed parameters. for
this new bond, I guess because tleap translate the residues to N-ter and
C-ter. Is there anyway to overcome it without tinkering the topology file?
The script I am using is:
source leaprc.ff12SB
loadamberparams frcmod.ionsjc_tip3p
mol = loadpdb protein_peptide.pdb
bond mol.228.C mol.241.N
addions mol Cl- 0
alignAxes mol
solvateBox mol TIP3PBOX 12
charge mol
saveAmberParm mol system_1.prmtop system_1.prmcrd
savepdb mol system_1_solvated.pdb
quit
And this is the output:
system_1> tleap
-I: Adding /Users/bin/amber/amber12/dat/leap/prep to search path.
-I: Adding /Users/bin/amber/amber12/dat/leap/lib to search path.
-I: Adding /Users/bin/amber/amber12/dat/leap/parm to search path.
-I: Adding /Users/bin/amber/amber12/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff12SB
----- Source: /Users/bin/amber/amber12/dat/leap/cmd/leaprc.ff12SB
----- Source of /Users/bin/amber/amber12/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: /Users/ikass/bin/amber/amber12/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /Users/bin/amber/amber12/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /Users/bin/amber/amber12/dat/leap/lib/amino12.lib
Loading library: /Users/bin/amber/amber12/dat/leap/lib/aminoct12.lib
Loading library: /Users/bin/amber/amber12/dat/leap/lib/aminont12.lib
Loading library: /Users/bin/amber/amber12/dat/leap/lib/nucleic12.lib
Loading library: /Users/bin/amber/amber12/dat/leap/lib/ions08.lib
Loading library: /Users/bin/amber/amber12/dat/leap/lib/solvents.lib
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters:
/Users/bin/amber/amber12/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
>
> mol = loadpdb protein_peptide.pdb
Loading PDB file: ./protein_peptide.pdb
(starting new molecule for chain B)
Added missing heavy atom: .R<CASN 241>.A<OXT 15>
total atoms in file: 1978
Leap added 1748 missing atoms according to residue templates:
1 Heavy
1747 H / lone pairs
> bond mol.228.C mol.241.N
> addions mol Cl- 0
12 Cl- ions required to neutralize.
Adding 12 counter ions to "mol" using 1A grid
Grid extends from solute vdw + 5.91 to 11.91
Resolution: 1.00 Angstrom.
grid build: 0 sec
(no solvent present)
Calculating grid charges
charges: 7 sec
Placed Cl- in mol at (28.57, 19.62, 41.65).
Placed Cl- in mol at (38.57, 42.62, 46.65).
Placed Cl- in mol at (-7.43, 32.62, 68.65).
Placed Cl- in mol at (37.57, 38.62, 61.65).
Placed Cl- in mol at (7.57, 36.62, 35.65).
Placed Cl- in mol at (29.57, 14.62, 52.65).
Placed Cl- in mol at (8.57, 16.62, 38.65).
Placed Cl- in mol at (-6.43, 45.62, 70.65).
Placed Cl- in mol at (7.57, 30.62, 83.65).
Placed Cl- in mol at (38.57, 23.62, 49.65).
Placed Cl- in mol at (19.57, 25.62, 31.65).
Placed Cl- in mol at (21.57, 11.62, 65.65).
Done adding ions.
>
> alignAxes mol
> solvateBox mol TIP3PBOX 12
Solute vdw bounding box: 45.051 51.165 59.148
Total bounding box for atom centers: 69.051 75.165 83.148
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 72.535 77.969 86.545 angstroms.
Volume: 489452.045 A^3
Total mass 238611.280 amu, Density 0.810 g/cc
Added 11736 residues.
>
>
> charge mol
Total unperturbed charge: 0.000000
Total perturbed charge: 0.000000
> saveAmberParm mol system_1.prmtop system_1.prmcrd
Checking Unit.
WARNING: There is a bond of 5.066425 angstroms between:
------- .R<NGLY 228>.A<C 8> and .R<CASN 241>.A<N 1>
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: C - N - C
Could not find angle parameter: N - C - N
Building proper torsion parameters.
Building improper torsion parameters.
total 763 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
> savepdb mol system_1_solvated.pdb
Writing pdb file: system_1_solvated.pdb
Converting N-terminal residue name to PDB format: NILE -> ILE
Converting C-terminal residue name to PDB format: CSER -> SER
Converting N-terminal residue name to PDB format: NGLY -> GLY
Converting C-terminal residue name to PDB format: CASN -> ASN
> quit
Quit
Thanks in advance,
Itamar
--
===========================================
| Itamar Kass, Ph.D.
| Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass.monash.edu
============================================
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Received on Mon Mar 11 2013 - 04:00:04 PDT
