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.
Sunny On Tue, Aug 18, 2009 at 6:01 PM, Johnny Lam <[email protected]> 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: [email protected] > >
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