shahrbanoo karbalaee wrote:
Dear justin
I made topology top for tfe with gromos53a5.and I solvated in spc and
40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I
get this error.(I edit the name of atoms with name in rtp file HT)
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "topol.top", line 57]:
No default Proper Dih. types
Cleaning up temporary file gromppsYSJRG
-------------------------------------------------------
Program grompp, VERSION 3.3.2
Source code file: toputil.c, line: 61
Fatal error:
Atomtype 'HO' not found!
-------------------------------------------------------
my topology file is attached.
In the topol.top you've provided, you define all the necessary components for
TFE, but then later call tfe.itp. Why? You've obviously got an inconsistency
somewhere.
Think of it this way - in a topol.top for a protein generated by pdb2gmx, you
don't generate all the protein parameters, then later on, call protein.itp
within topol.top! If you just have a system of TFE + water, then you can define
the TFE parameters at the beginning of the .top, then just call spc.itp later.
I'm betting that within tfe.itp lies the problem. Remove the call for tfe.itp
and see how it goes, because you've already defined everything you need.
-Justin
best
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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