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.
On Dec 7, 2007 11:57 AM, Shozeb Haider <[EMAIL PROTECTED]> wrote: > Hi, > > I was wondering if any has expertise in using Amber ff99SB port (Pande's > lab). I am currently using port for 3.3.1 version of gromacs. > > When I solvate my protein and run grompp to generate a tpr file, it > gives me the following error > > checking input for internal consistency... > calling /lib/cpp -traditional... > processing topology... > Generated 2628 of the 2628 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 2628 of the 2628 1-4 parameter combinations > Cleaning up temporary file gromppXORFn5 > ------------------------------------------------------- > Program grompp, VERSION 3.3 > Source code file: toppush.c, line: 1108 > > Fatal error: > [ file "/usr/share/gromacs/top/spc.itp", line 41 ]: > Atom index (1) in settles out of bounds (1-0) > ------------------------------------------------------- > > From what it seems that the program is unable to communicate with > spc.itp file. However that should not be the case since the program > routinely does that when I run using other gromacs force fields. I have > also explicitly included the /share/gromacs/top direcly as well > > I have the following lines in my preprocessor : > cpp = /lib/cpp -traditional ; prepocessor of the > current machine > include = -I/usr/share/gromacs/top > define = > > Any suggestions would be much appreciated. > > Many thanks > > Shozeb Haider > The London School of Pharmacy > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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