On 27/01/2012 9:50 PM, Anik Sen wrote:
Hello,
Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job.
please help.
The following is a part of the dna pdb file, which I am using:
ATOM 1 OH DG5 X 1 13.663 36.760 21.465 0.00 0.00
ATOM 2 CT DG5 X 1 14.791 36.040 21.150 0.00 0.00
ATOM 3 CT DG5 X 1 14.771 34.703 21.873 0.00 0.00
ATOM 4 OS DG5 X 1 16.017 34.553 22.577 0.00 0.00
ATOM 5 CT DG5 X 1 13.724 34.528 22.970 0.00 0.00
ATOM 6 OS DG5 X 1 13.540 33.118 23.234 0.00 0.00
The third column here is the atom name, the fourth is the residue name.
............................................................................................
I am using amber 03 forcefield (amber03.ff) whose atom type is as follows:
H0 1.00800 ; H aliph. bond. to C with 1 electrwd.
group (03GLY)
Br 79.90000 ; bromine
C 12.01000 ; sp2 C carbonyl group
CA 12.01000 ; sp2 C pure aromatic (benzene)
CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction
CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS
CK 12.01000 ; sp2 C 5 memb.ring in purines
CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6
..................................................................................................
The dna-rtp file in the amber 03 is as follows:
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove impropers over the same bond as a proper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 9 4 1 3 1 0
; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's
[ DA5 ]
[ atoms ]
H5T HO 0.44220 1
O5' OH -0.63180 2
C5' CT -0.00690 3
H5'1 H1 0.07540 4
............................................
[ DG5 ]
[ atoms ]
H5T HO 0.44220 1
O5' OH -0.63180 2
C5' CT -0.00690 3
H5'1 H1 0.07540 4
H5'2 H1 0.07540 5
C4' CT 0.16290 6
H4' H1 0.11760 7
O4' OS -0.36910 8
C1' CT 0.03580 9
...................................................
The first column here is the atom name, the second column is the atom
type. pdb2gmx has to be able to match atom names in the .pdb file with
those here, for the given residue. In your case, it can't. You will need
to rename the atoms in the .pdb file, somehow. When you do, make sure
you preserve the column formatting of the .pdb file.
Mark
But then also when I am running the file with the command:
pdb2gmx -f dna5.pdb -o dnA5.pdb -p topol.top
with TIP3P water model
I am getting the following error:
Identified residue DG51 as a starting terminus.
Warning: Residue Na2 in chain has different type (Ion) from starting
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting
residue DG51 (DNA).
Warning: Residue Na2 in chain has different type (Ion) from starting
residue DG51 (DNA).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue DG51 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.
Thanks in advance
========================================================
Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
www.csmcri.org
========================================================
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