On 2011-03-16 11.29, maria goranovic wrote:
Hello
I am trying to pdb2gmx with a free amino acid in amber99sb as follows:
pdb2gmx -f temp.pdb -ff amber99sb
there are no ter records in the input pdb file.
However, pdb2gmx fails with the following error:
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2gmx.c, line: 284
Fatal error:
In the chosen force field there is no residue type for 'GLU' as a
starting terminus
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Is this some kind of bug. If so, is there a workaround? For example, can
I have the amino acid bound to the terminus of the larger protein (for
which the free amino acid is a ligand) and make the bond have a zero
spring constant or something?
This is a missing feature in the FF. Since charges are different for
N-terminal and C-terminal residues in Amber there are separate
N-terminal and C-terminal variants of (almost) all residues, but not for
isolated AA. Your best bet is to use Antechamber to make a GAFF
topology which you can convert to gromacs again.
Maria
Maria G.
Technical University of Denmark
Copenhagen
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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