Marysa van den Berg wrote:
Hi,
The number of atoms in the second line of my .gro file are correct, I
checked that.
This is what my topology file says in the beginning:
[ moleculetype ]
; Name nrexcl
Protein 3
No changes here after the solvation.
At the end after the [ atoms ] directive:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong po
sition restraints for InflateGro
#ifdef STRONG_POSRES
#include "strong_posre.itp"
endif
Here's the problem. To end the #ifdef statement, you need "#endif", not
"endif." Since you haven't closed the #ifdef, nothing is being found after this
point in the topology (assuming you're not specifying "define = -DSTRONG_POSRES"
in the .mdp file, which you only want at certain times).
-Justin
; Include DPPC chain topology
#include "dppc.itp"
; Include water topology
#include "spc.itp"
#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
Protein
[ molecules ]
; Compound #mols
Protein 1
DPPC 242
SOL 48333
The only thing in the topology that changed after the solvation, was
adding the watermolecules in the [ molecules ] section (SOL 48333)
What could be the problem?
Thanks,
Marysa
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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