nahren manuel wrote:
<snip>
----
but i get the following error
* * * * *
Generated 380 of the 1326 non-bonded parameter combinations
ERROR 0 [file "top_A.itp", line 16530]:
No default Proper Dih. types
ERROR 0
[file "top_A.itp", line 16531]:
No default Proper Dih. types
Then you haven't added all of the proper dihedrals for that particular molecule
(phosphates are tricky). There is a parameter set (ffG43a1p) that has a
properly-derived set of parameters for phosphorylated amino acids in the User
Contributions on the web site.
I recall that not all of the formatting was quite right in these files (they
were designed for use with Gromacs 3.1.x, IIRC), so if you encounter errors you
can contact me off-list and I can send you re-formatted files that I have gotten
to work.
-Justin
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
NOTE:
System has non-zero total charge: -1.999996e+00
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# G96BONDS: 5789
# G96ANGLES: 8462
# PDIHS: 3040
# IDIHS: 2893
# LJ14: 9248
-------------------------------------------------------
Program grompp, VERSION 3.3.2
Source code file: grompp.c, line: 1182
Fatal error:
There were 2 errors in input file(s)
-------------------------------------------------------
"Ich Bin Ein Berliner" (J.F. Kennedy)
* * * * * *
Kindly advice
nahren
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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