[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

[Ye Yang]

Hi, everyone:
      I am a new user of Gromacs, and I am running through the tutorial.
When I am trying to run the ligand-receptor binding tutorial from

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
     I met some trouble in adding ion.
     Each time when I use genion, it shows:

Will try to add 0 NA ions and 6 CL ions.
Select a continuous group of solvent molecules
Group     0 (         System) has 33046 elements
Group     1 (        Protein) has  1693 elements
Group     2 (      Protein-H) has  1301 elements
Group     3 (        C-alpha) has   163 elements
Group     4 (       Backbone) has   489 elements
Group     5 (      MainChain) has   653 elements
Group     6 (   MainChain+Cb) has   805 elements
Group     7 (    MainChain+H) has   815 elements
Group     8 (      SideChain) has   878 elements
Group     9 (    SideChain-H) has   648 elements
Group    10 (    Prot-Masses) has  1693 elements
Group    11 (    non-Protein) has 31353 elements
Group    12 (          Other) has    15 elements
Group    13 (            JZ4) has    15 elements
Group    14 (          Water) has 31338 elements
Group    15 (            SOL) has 31338 elements
Group    16 (      non-Water) has  1708 elements
Select a group: 15
Selected 15: 'SOL'
Number of (3-atomic) solvent molecules: 10446

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.3#

-------------------------------------------------------
Program genion_d, VERSION 4.5.4
Source code file: gmx_genion.c, line: 285

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'

I checked my topology file and it looks fine:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spc.itp"

; Include ligand topoloty
#include "drg.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name

Protein
[ molecules ]
; Compound        #mols
Protein_chain_A     1
JZ4                 1
SOL             10446

One thing that might happen is in the genion source file,  I read through
it, and the problem either happens in loading the line to buf2, or in the
gmx_strcmp(buf2,"SOL"), since clearly the SOL_line is -1 aftermath.

The other thing I tried is to remove the ligand JZ4 part in both topology
and coordinates file, and in this case, it works perfectly for adding ion.
But in this way, I do not know how to insert my ligand into the system since
it might collide with solvent.

Can someone help me with this problem?

Thank you all very much.

Ye Yang
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110616/2793ea40/attachment.html>