[gmx-users] Re: dssp output of CG structure of 1K4C

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 19 00:11:45 CEST 2009

sunny mishra wrote:
> Hi Johny and Justin,
> Thanks for the reply. But another problem here arises regarding the 
> 1K4C_clean.top file. I have to minimize the system in vacuum i.e. 
> without adding any water molecules in it. After making the .gro file 
> from 1K4C_clean.pdb file with the help of genbox command and when I do 
> the grommp command it says that your .gro file does not match with the 
> .top file. But I can get rid of that by adding W molecules. It doesn't 

If you have to add waters to make the .gro match the .top, then water molecules 
have been added to the [molecules] section in the .top.  The real solution is to 
fix the [molecules] section to actually do an in vacuo minimization.


> make sense to me that when I am trying to minimize the system in vacuum 
> why do I have to add the water molecules or add anything else. They 
> should match...do you guys have any idea? Also, in my .top file I am 
> using the martini.itp file and also 1K4C_clean.itp file which I 
> generated from seq2itp.pl script after getting the .ssd files.
> Sunny
> On Tue, Aug 18, 2009 at 6:01 PM, Johnny Lam <johntus01 at gmail.com 
> <mailto:johntus01 at gmail.com>> wrote:
>     Hi Sunny,
>     Justin is right in saying that the hydrogen bonds will be absent in
>     the coarse grained file. For MARTINI, you would need to get the
>     secondary structure information from the original, un-CG .pdb file
>     (in your case, your 1K4C clean pdb file). When doing the topology,
>     it will become clear that the .ssd file that is required will be
>     that obtained from your original pdb file. That is how the MARTINI
>     force field works. I hope this helps!
>     Best,
>     --Johnny
>     -- 
>     -------------------------------------------------
>     Johnny Lam
>     ISPE Berkeley Chapter External Vice President
>     Department of Bioengineering
>     College of Engineering
>     University of California, Berkeley
>     Tel: (408) 655- 6829
>     Email: johntus at berkeley.edu <mailto:johntus at berkeley.edu>
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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


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