On 1/4/13 5:06 AM, Kieu Thu Nguyen wrote:
Thank Neha ! I follow your advices but this error still appear. I don't
know why.
You'll have to show us exactly what you're doing to get any solid advice.
Consider what I posted earlier. Usually the mismatch occurs because you are
using a coordinate file from some prior step in building your system that no
longer matches the actual system.
By the way, does anybody know why there are not ions in topology file in
Martini CG-MD. Because I see the system has not zero charge, i don't
understand why the CG system not be neutralized by ions.
There are ion parameters for MARTINI:
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters/60-ions
-Justin
Thanks and regards,
KT
On Fri, Jan 4, 2013 at 3:40 PM, Awasthi, Neha <
[email protected]> wrote:
First check your .gro file and your .top file, to make sure atom 6518 (or
Water) is consistently defined.
Next step would be to make sure this atom features in the index file
within a
"correct group".
In some cases, if a single atom is left out and not part of any group in
the
index file, it gives this error.
Why not make your index file again ?
Read the help provided with the command "make_ndx" to understand this.
Hope that works!
-----Original Message-----
From: [email protected] on behalf of Kieu Thu Nguyen
Sent: Fri 1/4/2013 6:51 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] error with indexfile
Dear All,
When using the command
grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
equilibrate.tpr
The error is
Fatal error:
Invalid atom number 6518 in indexfile
How can i fix this ?
Thank so much for any help !
Regards,
KT
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
