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.
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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