><deckuofm@yahoo.com><mark.abraham@anu.edu.au><gmx-users@gromacs.org>So look at your structures like I said last time! I'm not here to give<br />>my valuable time giving free advice in order to have it ignored...<br /><br />Thank you very much for your kindness and patience. Maybe sometimes my questions seems to be silly and boring, my knowledge about GROMACS is really lack, sorry.....<br /><br />Actually, I really cannot understand what you said yesterday. Did you mean is there any difference between the atom coordinates of ATP before- and after- minimization?  I found there are not any difference between these two structure.<br />(There are also not any obvious collision between atoms of ATP when represent it by Rasmol) <br /><br />> >mjduan@smail.hust.edu.cn wrote:<br />> <br />> >To reply to a list email, just reply as you would to any other email.<br />> <br />> <br />> >The .top succeeded in minimizing the solvated structure, so
that's a<br />> >good start. I think I can see that I was being too subtle for you<br />> >earlier with my suggestion that you think about observables that would<br />> >tell you whether your topology was working. Have you looked at the<br />> >before- and after-minimization structures to see whether they make <br />> >sense according to your training at recognizing chemical structures <br />> >that will be energy minima? If all of your components look reasonable post-minimization on their own,<br />  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^what means?<br />> > and there were no significant warnings<br />> >or errors from grompp then your topolog ies probably are OK too. <br />^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^just like I said in last email, there are not any warnning and error from grompp.<br /><br />> >Thenyou should go back and approach your original problem of getting <br />> >working topology f
or your combination system.<br />                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^I cannot run the full MD SImulation for ATP individually, so I think maybe there are something problem with it (I used the same minim.mdp can successfully do the energy minimization of the protein individually).  I really confused.<br />> <br />> >Mark<br /><mgoette@mpi-bpc.mpg.de><gmx-users@gromacs.org><http: evt="48518/*http://autos.yahoo.com/carfinder/;_ylc=X3oDMTE3NWsyMDd2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDY2FyLWZpbmRlcg--" us.rd.yahoo.com=""><mark.abraham@anu.edu.au><gmx-users@gromacs.org><fileti@ufabc.edu.br><mark.abraham@anu.edu.au><gmx-users@gromacs.org><br /><br /></gmx-users@gromacs.org></mark.abraham@anu.edu.au></fileti@ufabc.edu.br></gmx-users@gromacs.org></mark.abraham@anu.edu.au></http:></gmx-users@gromacs.org></mgoette@mpi-bpc.mpg.de></gmx-users@gromacs.org></mark
.abraham@anu.edu.au></deckuofm@yahoo.com>