Thank you, Justin!<br><br>I found the error message which was embedded in a lot of text. :P<br><br>As you said, the atom indexing is not a problem at all. The actual error is: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented<br>
<br>When I changed ns_type to grid, the problem was solved!<br><br>Thanks a lot!<br><br>Peggy<br><br><br><div class="gmail_quote">On Sat, Feb 14, 2009 at 4:26 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d"><br>
<br>
Peggy Yao wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Unfortunately, no. :( When I tried to add ions to the system using:<br>
<br>
grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr<br>
<br>
It return me an error without explanation:<br>
<br>
processing coordinates...<br>
double-checking input for internal consistency...<br>
<br>
There was 1 note<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.2<br>
Source code file: grompp.c, line: 864<br>
<br>
Fatal error:<br>
There were 1 error(s) processing your input<br>
-------------------------------------------------------<br>
<br>
Did I make any mistake? I am new to MD simulation and Gromacs. The following are all the steps that I ran until the fatal error:<br>
<br>
</blockquote>
<br></div>
Probably. Search the entire output of grompp for the error message. I don't remember grompp ever reporting a fatal error without printing the actual problem somewhere that the user can see.<br>
<br>
If you can provide that information, as well as the contents of your .mdp, there may be a chance to diagnose what's going on. As I said before, the problem *shouldn't* be the number of atoms in the file.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o 1eia.gro -water spce >& pdb2gmx.log<br>
# add water<br>
editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log<br>
genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >& genbox.log<br>
# add counter ions<br>
grompp -f em.mdp -c 1eia_water.gro -p 1eia.top -o 1eia_ion.tpr >& grompp_ion.log<br>
<br>
Peggy<br>
<br></div><div class="Ih2E3d">
On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
<br>
----- Original Message -----<br></div><div class="Ih2E3d">
From: Peggy Yao <<a href="mailto:peggy.yao@gmail.com" target="_blank">peggy.yao@gmail.com</a> <mailto:<a href="mailto:peggy.yao@gmail.com" target="_blank">peggy.yao@gmail.com</a>>><br>
Date: Sunday, February 15, 2009 10:24 am<br>
Subject: Re: [gmx-users] Atom index overflow after adding water<br></div><div><div></div><div class="Wj3C7c">
To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>, Discussion list for<br>
GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
> Thank you, Justin!<br>
><br>
> I changed the output files to .gro.<br>
><br>
> pdb2gmx -ignh -ff oplsaa -f 1eia_fixed.pdb -p 1eia.top -o<br>
1eia.gro -water spce >& pdb2gmx.log<br>
> # add water<br>
> editconf -bt cubic -f 1eia.gro -o 1eia.gro -c -d 0.9 >& editconf.log<br>
><br>
genbox -cp 1eia.gro -cs spc216.gro -o 1eia_water.gro -p 1eia.top >&<br>
genbox.log<br>
><br>
> However, the overflow error still occurs in the gro file:<br>
><br>
> 32448SOL HW299996 9.410 8.282 1.575<br>
> 32449SOL OW99997 9.923 8.813 0.726<br>
><br>
32449SOL HW199998 9.874 8.726 0.735<br>
> 32449SOL HW299999 9.900 8.856 0.639<br>
> 32450SOL OW 0 0.018 7.452 0.502<br>
> 32450SOL HW1 1 0.058 7.543 0.493<br>
> 32450SOL HW2 2 -0.082 7.460 0.508<br>
><br>
32451SOL OW 3 9.507 8.424 1.264<br>
> 32451SOL HW1 4 9.596 8.379 1.250<br>
><br>
> What's wrong? Thanks a lot!<br>
<br>
Probably nothing. The issue is whether the parsing algorithm in<br>
grompp will handle the situation gracefully. Justin thinks it does.<br>
You should try it and see :-)<br>
<br>
Mark<br>
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<br><div class="Ih2E3d">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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<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>
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