Thanks for the help.
I have change the atom type depending on gaff force field but still I
get the following error.
Sourcing: ./leap1.txt
----- Source: /home/pinak/amber14/dat/leap/cmd/leaprc.ff14SB
----- Source of /home/pinak/amber14/dat/leap/cmd/leaprc.ff14SB done
Log file: ./leap.log
Loading parameters: /home/pinak/amber14/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/pinak/amber14/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/pinak/amber14/dat/leap/lib/amino12.lib
Loading library: /home/pinak/amber14/dat/leap/lib/aminoct12.lib
Loading library: /home/pinak/amber14/dat/leap/lib/aminont12.lib
Loading library: /home/pinak/amber14/dat/leap/lib/nucleic12.lib
Loading library: /home/pinak/amber14/dat/leap/lib/atomic_ions.lib
Loading library: /home/pinak/amber14/dat/leap/lib/solvents.lib
Loading parameters: /home/pinak/amber14/dat/leap/parm/frcmod.tip4pew
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP4P
Loading parameters: /home/pinak/amber14/dat/leap/parm/frcmod.ionsjc_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung &
Cheatham JPCB (2008)
----- Source: /home/pinak/amber14/dat/leap/cmd/leaprc.gaff
----- Source of /home/pinak/amber14/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/pinak/amber14/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
Loading Prep file: ./sah.prep
Loading parameters: ./sah.parm
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Prep file: ./ias.prep
** This is a remark line: 'IMPROPER' atom OD2 not found
Loading parameters: ./ias.parm
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading PDB file: ./hpimt-adohcy-iasp1.pdb
Added missing heavy atom: .R<CLYS 226>.A<OXT 23>
Added missing heavy atom: .R<IAS 231>.A<OD1 11>
Added missing heavy atom: .R<CALA 233>.A<OXT 11>
total atoms in file: 1792
Leap added 1795 missing atoms according to residue templates:
3 Heavy
1792 H / lone pairs
Checking Unit.
ERROR: The unperturbed charge of the unit: -0.575400 is not integral.
WARNING: The unperturbed charge of the unit: -0.575400 is not zero.
-- ignoring the error and warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - n3
Could not find bond parameter for: c3 - N
Building angle parameters.
Could not find angle parameter: O - C - n3
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 - c3
Could not find angle parameter: CX - C - n3
Could not find angle parameter: oh - c3 - N
Could not find angle parameter: c3 - N - H
Could not find angle parameter: c3 - N - CX
Could not find angle parameter: c3 - c3 - N
Building proper torsion parameters.
** No torsion terms for O-C-n3-hn
** No torsion terms for O-C-n3-c3
** No torsion terms for CX-C-n3-hn
** No torsion terms for CX-C-n3-c3
** No torsion terms for oh-c3-N-H
** No torsion terms for oh-c3-N-CX
** No torsion terms for c3-c3-N-H
** No torsion terms for c3-c3-N-CX
Building improper torsion parameters.
old PREP-specified impropers:
<SAH 227>: CA O C OXT
<SAH 227>: C1' C4 N9 C8
<SAH 227>: H8 N9 C8 N7
<SAH 227>: C6 C4 C5 N7
<SAH 227>: C5 N1 C6 N6
<SAH 227>: C6 HN62 N6 HN61
<SAH 227>: H2 N1 C2 N3
<SAH 227>: C5 N9 C4 N3
<IAS 231>: -M CA N H
<IAS 231>: CA +M C O
total 687 improper torsions applied
10 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Total unperturbed charge: -0.575400
Total perturbed charge: -0.575400
Writing pdb file: hpimt_leap.pdb
Converting N-terminal residue name to PDB format: NALA -> ALA
Converting C-terminal residue name to PDB format: CLYS -> LYS
Converting N-terminal residue name to PDB format: NVAL -> VAL
Converting C-terminal residue name to PDB format: CALA -> ALA
On Mon, Feb 22, 2016 at 4:45 PM, Jesmita Dhar <dhar.beauty.gmail.com> wrote:
> After some modification in parameter file still I am getting the following error
> ERROR: The unperturbed charge of the unit: -0.281800 is not integral.
> WARNING: The unperturbed charge of the unit: -0.281800 is not zero.
>
> -- ignoring the error and warning.
>
> Building topology.
> Building atom parameters.
> For atom: .R<IAS 231>.A<H 2> Could not find vdW (or other) parameters
> for type: h
> For atom: .R<IAS 231>.A<OD1 11> Could not find vdW (or other)
> parameters for type: o2
> Parameter file was not saved.
> Total unperturbed charge: -0.281800
> Total perturbed charge: -0.281800
> Writing pdb file: hpimt_leap.pdb
> Converting N-terminal residue name to PDB format: NALA -> ALA
> Converting C-terminal residue name to PDB format: CLYS -> LYS
> Converting N-terminal residue name to PDB format: NVAL -> VAL
> Converting C-terminal residue name to PDB format: CALA -> ALA
> Quit
>
> On Mon, Feb 22, 2016 at 4:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> These are the critical lines.
>>
>> On 2/22/16 2:15 AM, Jesmita Dhar wrote:
>>> For atom: .R<IAS 231>.A<H 2> Could not find vdW (or other) parameters
>>> for type: h
>>> For atom: .R<IAS 231>.A<OD1 12> Could not find vdW (or other)
>>> parameters for type: o2
>> It appears you are missing vdw (or other) parameters, aside from a close
>> contact in your coordinate file and a nonintegral charge. For the
>> missing parameters, you could investigate gaff force field files that
>> might be loaded.
>>
>> Bill
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Feb 22 2016 - 04:00:04 PST
