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>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 class="gmail_quote">On Sat, Feb 14, 2009 at 3:31 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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>
----- Original Message -----<br>
From: Peggy Yao <<a href="mailto:peggy.yao@gmail.com">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>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">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 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 >& 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>
</div>Probably nothing. The issue is whether the parsing algorithm in grompp will handle the situation gracefully. Justin thinks it does. You should try it and see :-)<br>
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="Wj3C7c">_______________________________________________<br>
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