Yeah I agree wiht you but I tested another protein as well 1BL8 to check if there was a problem specifically in 1K4C. Even after testing 1BL8 it gives me the same error. What do you think?
On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sunny mishra wrote: > >> Dear all, >> >> I was earlier facing problem regarding the mismatch of atoms in .top and >> .gro file and then after useful discussion here I figured out that some >> atoms were missing in my cg.pdb file and that problem is because of the >> OLDER atom2cg.awk script which MARTINI folks have in their website. When I >> was using the earlier version of atom2cg.awk script I had 776 atoms in my >> .gro file and 804 atoms in .itp file and thats why .top and .gro were not >> matching but again the same problem raised even after using the new >> atom2cg.awk script which they sent me but it included some ILE residues and >> now I have 784 atoms in .gro file and 804 atoms in .itp file >> >> > As I recall, the root problem was that the original .pdb file from the RCSB > had missing atoms that you had not properly modeled back in. > > I pretty much now know how to fix the script but I am confused in some of >> the things like: >> >> 1) In the cleaned.pdb file of my protein the ARG residue in the >> atom2cg.awk script takes only CA, CG and NE with BN0, SC1, and SC2. If I >> want to include other atoms as well like NH1, NH2, CZ, CD etc what should I >> print for these atoms (either BN0, SC1, or SC2). As a matter of fact I don't >> know what do SC1, BN0, SC2 mean? >> > > Hence the point of CG. You don't account for every single atom that was in > the atomistic structure. BN0 = backbone particle, SC1 and SC2 are side > chain particles that will be given specific attributes in the topology. > > You should probably refer to the MARTINI publications for a more clear > understanding of how the force field was conceived and how it should be > used. > > -Justin > > So, i don't know while adding other atoms for ARG residue what should I >> print for them and I searched in the martini website but could not find >> anything. Please let me know if you got my problem. >> >> Thanks, >> >> Sunny >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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/mailing_lists/users.php >
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