Dear all
I want to do simulation with amber 10 (force field amber03) on protein-dna
complex.
1) $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
2) complex = loadpdb "complex.pdb"
Loading PDB file: ./complex.pdb
Created a new atom named: H within residue: .R<NGLY 7>
Created a new atom named: HA1 within residue: .R<NGLY 7>
Created a new atom named: HB1 within residue: .R<LYS 8>
Created a new atom named: HG1 within residue: .R<LYS 8>
Created a new atom named: HD1 within residue: .R<LYS 8>
Created a new atom named: HE1 within residue: .R<LYS 8>
Created a new atom named: HA1 within residue: .R<GLY 9>
.
.
.
.
.
Created a new atom named: HB1 within residue: .R<TRP 62>
Created a new atom named: HB1 within residue: .R<ARG 63>
Created a new atom named: HG1 within residue: .R<ARG 63>
Created a new atom named: HD1 within residue: .R<ARG 63>
Created a new atom named: HB1 within residue: .R<ARG 64>
Created a new atom named: HG1 within residue: .R<ARG 64>
Created a new atom named: HD1 within residue: .R<ARG 64>
Created a new atom named: OC1 within residue: .R<SER 65>
Created a new atom named: HB1 within residue: .R<SER 65>
Added missing heavy atom: .R<SER 65>.A<O 11>
Created a new atom named: HA1 within residue: .R<CGLY 66>
Added missing heavy atom: .R<CGLY 66>.A<OXT 8>
Illegal CONECT record in pdb file
Illegal CONECT record in pdb file
total atoms in file: 1864
Leap added 114 missing atoms according to residue templates:
2 Heavy
112 H / lone pairs
The file contained 111 atoms not in residue templates
---------------------------------------------------------------------
I continued following steps:
3) addions complex Na+ 0
4) solvatebox complex TIP3PBOX 8.0 iso
5) saveamberparm complex complex.prmtop complex.inpcrd
But I encountered with
Checking Unit.
WARNING: There is a bond of 0.430932 angstroms between:
------- .R<ILE 20>.A<CA 3> and .R<ILE 20>.A<HA 4>
WARNING: There is a bond of 0.470151 angstroms between:
------- .R<TYR 31>.A<N 1> and .R<TYR 31>.A<H 2>
WARNING: There is a bond of 0.342126 angstroms between:
------- .R<LYS 42>.A<CD 11> and .R<LYS 42>.A<HD2 12>
WARNING: There is a bond of 0.478428 angstroms between:
------- .R<ARG 49>.A<NE 14> and .R<ARG 49>.A<HE 15>
WARNING: The unperturbed charge of the unit: -14.000000 is not zero.
FATAL: Atom .R<NGLY 7>.A<H 10> does not have a type.
FATAL: Atom .R<NGLY 7>.A<HA1 11> does not have a type.
FATAL: Atom .R<LYS 8>.A<HB1 23> does not have a type.
FATAL: Atom .R<LYS 8>.A<HG1 24> does not have a type.
FATAL: Atom .R<LYS 8>.A<HD1 25> does not have a type.
FATAL: Atom .R<LYS 8>.A<HE1 26> does not have a type.
FATAL: Atom .R<GLY 9>.A<HA1 8> does not have a type.
.
.
.
.
.
FATAL: Atom .R<TRP 62>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 63>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 63>.A<HG1 26> does not have a type.
FATAL: Atom .R<ARG 63>.A<HD1 27> does not have a type.
FATAL: Atom .R<ARG 64>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 64>.A<HG1 26> does not have a type.
FATAL: Atom .R<ARG 64>.A<HD1 27> does not have a type.
FATAL: Atom .R<SER 65>.A<OC1 12> does not have a type.
FATAL: Atom .R<SER 65>.A<HB1 13> does not have a type.
FATAL: Atom .R<CGLY 66>.A<HA1 9> does not have a type.
Failed to generate parameters
Parameter file was not saved.
--------------------------------------------------------------------------------------------------------
In my opinion, before loadpdb step, I should do some changes in complex.pdb
file.
To obtain accordance between residues in pdb file and rsidues in templates,
I compared my pdb file with
all_amino03.in file. Then I did changes in pdb file so that after loadpdb
step,
Loading PDB file: ./complex.pdb
total atoms in file: 1868
Rest of steps were done without any error.
To visualize my generated prmtop/coordinate file to make sure the topology
of system appears correct, I used
$AMBERHOME/exe/ambpdb -p complex.prmtop < complex.inpcrd > complex_new.pdb.
When I saw complex_new.pdb with VMD program, some bonds are broken and some
atoms are as a point.
I saw complex.pdb in which I made some changes with VMD. unfortunately, it
is also similar to complex_new.pdb.
how to obtain prmtop and inpcrd files truely without any error from
initial pdb file?
any help will highly appreciated.
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Received on Tue Jan 31 2012 - 06:30:54 PST
