Quoting #NGUYEN CONG TRI# <[EMAIL PROTECTED]>: > 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 > <mailto: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?
It is likely due to bad contacts. Check the list archives for relevant discussions (there are many). Try a thorough energy-minimization of your system to relax bad contacts. -Justin > > Is there anyone experienced in this problem, could you please give me some > advice, I really appreciate. > > Best regards, > Tri. > > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
