On 2010-08-16 14.44, Maiki wrote:
David van der Spoel wrote:
On 2010-08-16 12.34, Maiki wrote:
So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.
Not all force fields have complete support for DNA. Try Charmm.
I tried all the forces I got with gromacs and they all failed with
different errors (ok, amber worked, but I wanted to try gromos for some
reasons). For charmm the error was:
"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."
did you run with the -ter option and select none?
so, it looks that charmm also tries to find N- and C- termini (or I
don't understand the error message which is also more than possible)
Besides, gromos does recognise DNA base pairs (DTHY for thymine etc,
they are in ff files) and all its atoms, only in the end it asks this
stupid question 'where is my NH3+ group?' and fails...
There may be something with my pdb format but that's what I got from
rcsb/pdb. Is there a canonical description of PDB format expected by ffs
in pdb2gmx so I could correct my input myself? (if it's going to help)
Maiki wrote:
Hi,
I'm trying to convert protein-DNA complex using pdb2gmx with
gromos53a6.ff
$ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh
In gromacs version 4.5-beta2 the result is:
Processing chain 3 'C' (516 atoms, 25 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DT1 as a starting terminus.
Identified residue DA25 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Warning: 'DT' not found in residue topology database, trying to use
'DTHY'
Start terminus: NH3+
Warning: 'DA' not found in residue topology database, trying to use
'DADE'
End terminus: COO-
Warning: 'DT' not found in residue topology database, trying to use
'DTHY'
Warning: 'DA' not found in residue topology database, trying to use
'DADE'
Warning: 'DG' not found in residue topology database, trying to use
'DGUA'
(...)
Warning: 'DA' not found in residue topology database, trying to use
'DADE'
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5-beta2
Source code file: pdb2top.c, line: 922
Fatal error:
atom N not found in buiding block 1DT while combining tdb and rtp
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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