Hi Marc, I figured it out. I tried upir suggestion and tested the gmxcheck but got the following errors
gmxcheck.exe -s1 topol.tpr Please give me TWO run input (.tpr/.tpa/.tpb) files or specify the -m flag to generate a methods.tex file gmxcheck.exe -s1 topol.tpr -m ------------------------------------------------------- Program gmxcheck, VERSION 4.0.5 Source code file: tpxio.c, line: 1643 Fatal error: Can not read file topol.tpr, this file is from a Gromacs version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible ------------------------------------------------------- gcq#332: Thanx for Using GROMACS - Have a Nice Day But then decided I need to run the grompp on my clients along with the pre-processing libraries generated by acpypi. Then tested the mdrun on the .tpr this generated. Then it was missing the aminoacids.dat I downloaded it and everything seems to work. I will now make some additional steps on this workflow so this should now work! Thanks again for your help I very much appreciate it. On Sun, Dec 27, 2009 at 7:18 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Jack Shultz wrote: >> >> If I preped the tpr using amber forcefields, could that be the reason? > > No. > >> The mdrun I am using does not have any force field libraries in its >> directory. > > That's irrelevant. Only non-mdrun tools care about the contents of $GMXLIB > or local force field files. The point of GROMPP is that it is the GROMacs > Pre-Processor that does all such for mdrun. > > When you get some advice, it's good politics to be seen to follow those up > (or reject with reasons) before casting about wildly with other theories :-) > You don't want the people giving free advice feeling like you're wasting > their time! > > Mark > >> On Sat, Dec 26, 2009 at 11:57 PM, Mark Abraham <mark.abra...@anu.edu.au> >> wrote: >>> >>> Jack Shultz wrote: >>>> >>>> I preped this ligand using acpypi followed by grompp >>>> grompp -f em.mdp -c ligand_GMX.gro -p ligand_GMX.top >>>> I tested this .tpr file on my server. WheI had another computer run it >>>> I get the following message. However we are using the same versions of >>>> gromacs. >>>> >>>> Back Off! I just backed up md.log to ./#md.log.2# >>>> >>>> ------------------------------------------------------- >>>> Program mdrun, VERSION 4.0.5 >>>> Source code file: tpxio.c, line: 1643 >>>> >>>> Fatal error: >>>> Can not read file topol.tpr, >>>> this file is from a Gromacs version which is older than 2.0 >>>> Make a new one with grompp or use a gro or pdb file, if >>>> possible >>>> ------------------------------------------------------- >>> >>> I'd say it's evident that if the file is not corrupted (use gmxcheck), >>> the >>> GROMACS installations weren't the same (unmodified) version. Reproduce >>> the >>> conditions and run grompp -h to inspect the version. >>> >>> Perhaps you are having a problem with a shared-library mismatch. >>> >>> If you have such an old version of GROMACS around, either uninstall it >>> and >>> retire the sysadmin, or send the computer to a museum :-) >>> >>> Mark >>> >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php