<div dir="ltr">Thank you for your suggestions.<br>I have checked the topology file with vim, and it looks pefectly, also, the only problem happens when I use genion. One thing that might be possible is that I use the double precision version of gromacs, because when I solve it in water, the written of topology file looks weired(like I showed).<br>
What do you mean by work-around? You mean just manually change some water molecules in topology file and coordinate file into ions? Will the program recognize something like CL, NA? Or can I just add ions to the system and solve it in water?<br>
<br>Thank you very much<br><br>Best<br>Wishes<br><br>Ye<br><br><div class="gmail_quote">2011/6/16 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Ye Yang wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi, everyone:<br>
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<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html</a><br>
I met some trouble in adding ion.<br>
Each time when I use genion, it shows:<br>
<br>
Will try to add 0 NA ions and 6 CL ions.<br>
Select a continuous group of solvent molecules<br>
Group 0 ( System) has 33046 elements<br>
Group 1 ( Protein) has 1693 elements<br>
Group 2 ( Protein-H) has 1301 elements<br>
Group 3 ( C-alpha) has 163 elements<br>
Group 4 ( Backbone) has 489 elements<br>
Group 5 ( MainChain) has 653 elements<br>
Group 6 ( MainChain+Cb) has 805 elements<br>
Group 7 ( MainChain+H) has 815 elements<br>
Group 8 ( SideChain) has 878 elements<br>
Group 9 ( SideChain-H) has 648 elements<br>
Group 10 ( Prot-Masses) has 1693 elements<br>
Group 11 ( non-Protein) has 31353 elements<br>
Group 12 ( Other) has 15 elements<br>
Group 13 ( JZ4) has 15 elements<br>
Group 14 ( Water) has 31338 elements<br>
Group 15 ( SOL) has 31338 elements<br>
Group 16 ( non-Water) has 1708 elements<br>
Select a group: 15<br>
Selected 15: 'SOL'<br>
Number of (3-atomic) solvent molecules: 10446<br>
<br>
Processing topology<br>
<br>
Back Off! I just backed up temp.top to ./#temp.top.3#<br>
<br>
-------------------------------------------------------<br>
Program genion_d, VERSION 4.5.4<br>
Source code file: gmx_genion.c, line: 285<br>
<br>
Fatal error:<br>
No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top'<br>
<br>
</blockquote>
<br></div></div>
Something doesn't match up here - the command backs up temp.top, but then complains it can't find SOL in topol.top. Either genion is looking at the wrong file or your command is somehow wrong.<div><div></div><div class="h5">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I checked my topology file and it looks fine:<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
; Include water topology<br>
#include "gromos43a1.ff/spc.itp"<br>
<br>
; Include ligand topoloty<br>
#include "drg.itp"<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
; Include topology for ions<br>
#include "gromos43a1.ff/ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
<br>
Protein<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_chain_A 1<br>
JZ4 1 SOL 10446<br>
<br>
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.<br>
<br>
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.<br>
<br>
</blockquote>
<br></div></div>
If removal of the JZ4 line relieves the problem, perhaps there's a problem with that line, i.e. the line ending? What type of system are you using? Sometimes Windows line endings cause problems. Always use a plain text editor and use dos2unix to process text files if you're on Windows.<br>
<br>
Otherwise, the work-around is to not have genion work on the topology. Make the corrections yourself. Simple addition of ions and subtraction of water molecules is trivial.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Can someone help me with this problem?<br>
<br>
Thank you all very much.<br>
<br>
Ye Yang<br>
<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br></div>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote></div><br></div>