[gmx-users] A query

[Mark Abraham]

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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