I need the rest of the structure just as it is now because I want to do electrostatic analysis with it. I just added the phosphate manually and so I want to minimize and run a short MD with it.
I added the dihedraltype of the amber database (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) to the ffbonded file. And additionally I looked at the protein and made all the residues which could somehow influence the protein flexible so that eventual clashes can be repaired. But still I got the error: ..Step 3612, time 3.612 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000008, max 0.000031 (between atoms 975 and 978) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976 979 32.6 0.0961 0.0960 0.0960 Step 3613, time 3.613 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000237, max 0.001400 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976 979 33.4 0.0960 0.0959 0.0960 .. Too many LINCS warnings (1000) I already minimized the protein and everything was fine. There were no errors: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 gcq#49: "You Could Make More Money As a Butcher" (F. Zappa) Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.7436938e+05 Maximum force = 8.6871973e+03 on atom 979 Norm of force = 7.1224258e+01 And also during the grompp run there are no errors. Can you please help me to find out where the problem lies? Thank you, Eva > > > On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Ah okey. Thank you. >> I will write them. >> >> Hmm, but the protein is a crystal structure from pdb with a resolution >> of >> 1.2. I already added the hydrogen atoms to this structure and there I >> already minimized them and made a md run. And there were no errors. And >> now I only added the phosphate to the minimized structure. So I thought >> that I only had to minimize the phosphate and the residue it bound on. >> Or is there a mistake in my thought here? > > If adding the phosphate resulted in a crash, then clearly that's the > problem. I > don't understand why you would run EM on just the phosphate and keep the > rest of > the protein structure frozen. Again, that potentially prevents clashes > from > being resolved. I don't understand what value there is in only minimizing > the > phosphate. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists