[gmx-users] error in ATOM2CG.awk script

[sunny mishra]

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
> 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 at 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-request at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090827/8cc3b5c6/attachment.html>