no i have given the right path only even i have checked the top file 2 do that first md run can make any harmful changes in top file
On 4/12/06, Mark Abraham <[EMAIL PROTECTED]> wrote: > santosh naik wrote: > > hi guys > > i am working with the spider toxin protein and as mentioned early i > > was unable 2 over come this process > > > > below i have mentioning my problem in detail > > Thanks for that. It looks OK to me. > > I've snipped out the lines where you mention the .top file > > grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr > > > > now again i run the grompp > > now here i have edited the top file > > i removed 2 water molecule and added 2 cl molecules > > grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr > > > > grompp -f pr.mdp -c 7/out7.gro -p 1/out1.top -o 8/out8.tpr > > > > here i got he error > > > > Fatal error: > > number of coordinates in coordinate file (7/out7.gro, 7485) > > does not match topology (1/out1.top, 0) > > So assuming that the contents of 1/out1.top haven't changed since you > edited them, the normal reason for it failing is that it can no longer > find the .itp files it needs to include. It found them earlier though, > so I expect something has changed about the environment. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
