Does the pdb file have alternative conformations for some side chains or atoms?
Like a side chain may have 50% chance to be rotated left, and 50% chance to be rotated right. The crystallographer recognized these two possibilities, and give each possibility a 0.5 occupancy. It may look like LYSA LYSB with A for one conformation, and B for another conformation. On Fri, Oct 17, 2014 at 6:08 PM, Agnivo Gosai <agnivogromac...@gmail.com> wrote: > Dear Gromacs Users > > I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO ) > . I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported > into it. I had cleaned the PDB file off crystal waters and a small chemical > ligand ( which I dont require ) before passing it through pdb2gmx. > > The topology has been successfully generated. > > However I am concerned with the following comments in the output of pdb2gmx > , I am copy pasting 3 blocks from the output :- > > ############################# > There are 3 chains and 0 blocks of water and 247 residues with 2590 atoms > > chain #res #atoms > 1 'D' 15 315 > 2 'L' 27 222 > 3 'H' 253 2053 > > WARNING: there were 0 atoms with zero occupancy and 9 atoms with > occupancy unequal to one (out of 2590 atoms). Check your pdb file. > ################################# > Processing chain 3 'H' (2053 atoms, 253 residues) > Analysing hydrogen-bonding network for automated assignment of histidine > protonation. 395 donors and 366 acceptors were found. > There are 535 hydrogen bonds > Will use HISE for residue 57 > Will use HISE for residue 71 > Will use HISE for residue 91 > Will use HISE for residue 119 > Will use HISE for residue 230 > Now there are 253 residues with 4078 atoms > ############################################ > Chain time... > Making bonds... > Warning: Long Bond (2429-2431 = 0.805851 nm) > Number of bonds was 4137, now 4136 > ##########################3 > > I would like to know the meaning of these messages. Also I am reading the > GROMACS manual for further info. > > Best , > > Agnivo > Iowa State , USA > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.