On 2013-04-18 21:35, Justin Lemkul wrote:
On 4/18/13 3:32 PM, Warren Gallin wrote:
Hi,
I'm not clear on how to use pdb2gmx to set up a small molecule for
simulation, or perhaps the limitations on this capability. My
understanding from the latest documentation and the 2013 publication
is that v4.5 is capable of handling non-protein/nucleic acid as input.
I have created a pdb file for my molecule of interest, but when I
invoke pdb2gmx as follows:
pdb2gmx -f BrMT_mono_nores.pdb -water tip4
I get a Fatal error message because there is no residue name (it's
neither protein or nucleic acid):
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file:
/Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581
Fatal error:
Residue '' not found in residue topology database
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
and just above that message there is also a Warning in the message
saying:
Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the
behavior.
8 out of 8 lines of specbond.dat converted successfully
Is there some documentation that specifically addresses the methods
and issues with using pdb2gmx for non-protein/nucleic acid molecules?
pdb2gmx only knows how to handle what it knows about. There is no
generic support for arbitrary compounds.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
Try GAFF using the Ambertools and acpype.
--
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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