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David van der Spoel wrote:
<blockquote cite="mid:4C693462.1010108@xray.bmc.uu.se" type="cite">On
2010-08-16 14.44, Maiki wrote:
<br>
<blockquote type="cite">David van der Spoel wrote:
<br>
<blockquote type="cite">On 2010-08-16 12.34, Maiki wrote:
<br>
<blockquote type="cite">So, anybody knows why it does that or how
to deal with nucleic acids?
<br>
I only saw one similar question asked recently (with different error)
<br>
which was also left without answer.
<br>
</blockquote>
Not all force fields have complete support for DNA. Try Charmm.
<br>
</blockquote>
I tried all the forces I got with gromacs and they all failed with
<br>
different errors (ok, amber worked, but I wanted to try gromos for some
<br>
reasons). For charmm the error was:
<br>
<br>
"There is a dangling bond at at least one of the terminal ends and
<br>
the force field does not provide terminal entries or files. Edit a
<br>
.n.tdb and/or .c.tdb file."
<br>
</blockquote>
<br>
did you run with the -ter option and select none?
<br>
</blockquote>
I did now, and it changed nothing for charmm.<br>
To be more precise it died before even asking me for dna termini.<br>
the last part of output is:<br>
<blockquote>Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.r2b<br>
Reading pfv-dna.pdb...<br>
Read 738 atoms<br>
Analyzing pdb file<br>
Splitting PDB chains based on TER records or changing chain id.<br>
There are 2 chains and 0 blocks of water and 17 residues with 738 atoms<br>
<br>
chain #res #atoms<br>
1 'C' 19 392 <br>
2 'D' 17 346 <br>
<br>
All occupancies are one<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/atomtypes.atp<br>
Atomtype 1<br>
Reading residue database... (charmm27)<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.rtp<br>
Residue 41<br>
Sorting it all out...<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/dna.rtp<br>
Residue 53<br>
Sorting it all out...<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/lipids.rtp<br>
Residue 65<br>
Sorting it all out...<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/rna.rtp<br>
Residue 77<br>
Sorting it all out...<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.hdb<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/lipids.hdb<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.n.tdb<br>
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.c.tdb<br>
<br>
Back Off! I just backed up pfv.top to ./#pfv.top.10#<br>
Processing chain 1 'C' (392 atoms, 19 residues)<br>
There are 0 donors and 0 acceptors<br>
There are 0 hydrogen bonds<br>
Identified residue DA1 as a starting terminus.<br>
Identified residue DA19 as a ending terminus.<br>
8 out of 8 lines of specbond.dat converted successfully<br>
No suitable end (N or 5') terminus found in database - assuming this
residue<br>
is already in a terminus-specific form and skipping terminus selection.<br>
No suitable end (C or 3') terminus found in database - assuming this
residue<br>
is already in a terminus-specific form and skipping terminus selection.<br>
-------------------------------------------------------<br>
Program pdb2gmx_d, VERSION 4.5-beta2<br>
Source code file: pdb2top.c, line: 883<br>
<br>
Fatal error:<br>
There is a dangling bond at at least one of the terminal ends and the
force field does not provide terminal entries or files. Edit a .n.tdb
and/or .c.tdb file.<br>
For more information and tips for troubleshooting, please check the
GROMACS<br>
website at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
</blockquote>
I removed chain A(protein) and hetatms, only left C and D of double DNA
helix.<br>
<br>
<blockquote cite="mid:4C693462.1010108@xray.bmc.uu.se" type="cite">
<blockquote type="cite"><br>
so, it looks that charmm also tries to find N- and C- termini (or I
<br>
don't understand the error message which is also more than possible)
<br>
Besides, gromos does recognise DNA base pairs (DTHY for thymine etc,
<br>
they are in ff files) and all its atoms, only in the end it asks this
<br>
stupid question 'where is my NH3+ group?' and fails...
<br>
<br>
There may be something with my pdb format but that's what I got from
<br>
rcsb/pdb. Is there a canonical description of PDB format expected by
ffs
<br>
in pdb2gmx so I could correct my input myself? (if it's going to help)
<br>
<br>
<blockquote type="cite">
<blockquote type="cite"><br>
Maiki wrote:
<br>
<blockquote type="cite">Hi,
<br>
<br>
I'm trying to convert protein-DNA complex using pdb2gmx with
<br>
gromos53a6.ff
<br>
<br>
$ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh
<br>
<br>
In gromacs version 4.5-beta2 the result is:
<br>
<br>
Processing chain 3 'C' (516 atoms, 25 residues)
<br>
There are 0 donors and 0 acceptors
<br>
There are 0 hydrogen bonds
<br>
Identified residue DT1 as a starting terminus.
<br>
Identified residue DA25 as a ending terminus.
<br>
8 out of 8 lines of specbond.dat converted successfully
<br>
Warning: 'DT' not found in residue topology database, trying to use
<br>
'DTHY'
<br>
Start terminus: NH3+
<br>
Warning: 'DA' not found in residue topology database, trying to use
<br>
'DADE'
<br>
End terminus: COO-
<br>
Warning: 'DT' not found in residue topology database, trying to use
<br>
'DTHY'
<br>
Warning: 'DA' not found in residue topology database, trying to use
<br>
'DADE'
<br>
Warning: 'DG' not found in residue topology database, trying to use
<br>
'DGUA'
<br>
(...)
<br>
Warning: 'DA' not found in residue topology database, trying to use
<br>
'DADE'
<br>
<br>
-------------------------------------------------------
<br>
Program pdb2gmx, VERSION 4.5-beta2
<br>
Source code file: pdb2top.c, line: 922
<br>
<br>
Fatal error:
<br>
atom N not found in buiding block 1DT while combining tdb and rtp
<br>
For more information and tips for troubleshooting, please check the
<br>
GROMACS
<br>
website at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a>
<br>
-------------------------------------------------------
<br>
<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
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