Regarding amb2gmx.pl, it should work for converting whole systems from Amber, but this may depend on the box geometry you are using. In particular I think it is OK with cubic boxes but not some of the more fancy geometries. The other option is just to convert your protein+ligand and solvate using gromacs tools.
David On Mon, Mar 10, 2008 at 10:31 PM, #NGUYEN CONG TRI# <[EMAIL PROTECTED]> wrote: > > > Dear all, > > I'm trying to study the interaction between NADH and a protein. And because > the parameters for NADH have been developed in amber99 and amber94 force > fields, so I just used the contributed parameter files for my simulation. > The coordinates I got from docking results. > > I made my whole system, including the protein and ligand in amber, and > generated, say complex.inpcrd and complex.prmtop. Then I used the > distributed amb2gmx.pl distributed elsewhere to convert them into > complex.gro and complex.top. It seems to be work well. But I'm not sure > whether it is appropriate to do that because my system is very big (the > protein with 5000 atoms and NADH 71 atoms, plus solvent). I notice that > amb2gmx.pl was only tested for small molecules. > > One more thing, I tried to run the minimization but maybe there is very > close contact between the ligand and the protein so the minimization failed. > The close contact maybe due to the added hydrogen atoms by amber, which were > trimed away upon docking. > Below is the error: > Variable ci has value -2147483648. It should have been within [ 0 .. 1728 ] > Please report this to the mailing list (gmx-users@gromacs.org) > Does the problem comes from close contact between NADH and the protein or > anything else? If it the case, then what should I do, because I cannot > arbitrarily re-position the ligand, can I? > > Is there anyone experienced in this problem, could you please give me some > advice, I really appreciate. > > Best regards, > Tri. > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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