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

sunny mishra mishra.sunny at gmail.com
Wed Aug 19 00:09:11 CEST 2009

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 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.


On Tue, Aug 18, 2009 at 6:01 PM, Johnny Lam <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
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