shahrbanoo karbalaee wrote:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
; Include water topology
#include "spce.itp"
Include tfe topology
#include "tfe.itp"
#endif
Well, there's the problem. You've enclosed the SPC/E and TFE .itp files within
an #ifdef/#endif block, so they only get included with -DPOSRES. Move spce.itp
and tfe.itp from within this block and things should work fine.
-Justin
#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
PEPTIDE A5 OR AUREIN 1.2 in 30%tfe water
[ molecules ]
; Compound #mols
Protein_A 1
SOL 941
tfe 301
---------------------------------------------------
and the file tfe.gro is:
Glycine aRginine prOline Methionine Alanine Cystine Serine
9
1TFE CC' 1 -0.098 -0.156 0.352
1TFE FD' 2 -0.010 -0.129 0.451
1TFE FE' 3 -0.143 -0.282 0.370
1TFE FF' 4 -0.203 -0.072 0.366
1TFE CB' 5 -0.033 -0.140 0.217
1TFE HB'1 6 -0.106 -0.161 0.139
1TFE HB'2 7 0.051 -0.209 0.209
1TFE O2' 8 0.014 -0.006 0.204
1TFE HO2 9 0.055 0.005 0.118
0.00000 0.00000 0.00000
thanks and best regards
--
========================================
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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