[gmx-users] A query

[Anik Sen]

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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