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
............................................................................................
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
...................................................
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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