On 9/12/12 1:58 AM, sarah k wrote:
Dear all,
I'm trying to simulate several drug-protein complexes on a clustered
server. I used PRODRG and editted my .top, .pdb, .gro and posre.itp files.
Here is the final lines of my .top file:
; Include Position restraint file
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
; Include Dio topology
#include "dio.top"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Nona in water
[ molecules ]
; Compound #mols
Protein_X 1
Dio 1
SOL 63598
The statements are closed with #endif. Yet I recieve "No molecules were
defined in the system". For the same file I sometimes get "No such molecule
type Dio" in the first grompp prompt. What's the solution?
Your topology is misformatted somewhere, either with an #ifdef/#endif block not
being closed properly or a naming inconsistency somewhere. The error is not
apparent from the snippet you've shown, so the best any of us can do is guess at
this point.
Beware that PRODRG topologies require considerable manual adjustment to be
considered sufficiently accurate.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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