[gmx-users] error in ATOM2CG.awk script
mishra.sunny at gmail.com
Thu Aug 27 23:12:48 CEST 2009
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 <jalemkul at 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
> 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.
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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