I used amber ff99 port with ffamber_tip3p.tip and it's works fine. I changed this in my molecule topology file. Up to now, nobody can say me why using tip3p with amber ports doesn't work.<br><br><div class="gmail_quote">
On Dec 7, 2007 11:57 AM, Shozeb Haider <<a href="mailto:shozeb.haider@pharmacy.ac.uk">shozeb.haider@pharmacy.ac.uk</a>> 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,<br><br>I was wondering if any has expertise in using Amber ff99SB port (Pande's<br>lab). I am currently using port for 3.3.1 version of gromacs.<br><br>When I solvate my protein and run grompp to generate a tpr file, it
<br>gives me the following error<br><br>checking input for internal consistency...<br>calling /lib/cpp -traditional...<br>processing topology...<br>Generated 2628 of the 2628 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge =
0.5<br>Generated 2628 of the 2628 1-4 parameter combinations<br>Cleaning up temporary file gromppXORFn5<br>-------------------------------------------------------<br>Program grompp, VERSION 3.3<br>Source code file: toppush.c
, line: 1108<br><br>Fatal error:<br>[ file "/usr/share/gromacs/top/spc.itp", line 41 ]:<br> Atom index (1) in settles out of bounds (1-0)<br>-------------------------------------------------------<br>
<br> From what it seems that the program is unable to communicate with<br>spc.itp file. However that should not be the case since the program<br>routinely does that when I run using other gromacs force fields. I have<br>also explicitly included the /share/gromacs/top direcly as well
<br><br>I have the following lines in my preprocessor :<br>cpp = /lib/cpp -traditional ; prepocessor of the<br>current machine<br>include = -I/usr/share/gromacs/top<br>define =<br>
<br>Any suggestions would be much appreciated.<br><br>Many thanks<br><br>Shozeb Haider<br>The London School of Pharmacy<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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