[gmx-users] constraining secondary structure gmx 5

[Smith, Micholas D.]

Hi, 

If the molecules have been parameterized in OPLS/Amber and Charmm, going from Charmm to OPLS/Amber is pretty straightforward, you just to build a topology using the OPLS/Amber atom-types instead of Charmm that correspond to your system (its just an elaborate find/replace exercise). For peptides it is even easier, as you can take your pdb of your peptide and run it through gmx pdb2gmx and select OPLS or Amber instead of Charmm as your force-field and it will generate a .gro file of your peptide and a topology file for the peptide with the proper atomtypes for the force-field.

-Micholas

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Yoav Atsmon-Raz <yoav.atsmonraz at ucalgary.ca>
Sent: Thursday, December 10, 2015 11:37 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] constraining secondary structure gmx 5

Thanks for your reply Micholas,

The secondary structure constraints are used to "guide" the structure to a known minimum so to speak and that particular structure is of interest to me. I never worked with OPLS or Amber, is the process of working with them equivalent to using charmm via gromacs? At least for the time being, working with something that I know will give me the results I'm interested in seems preferable to trying out alternative software that I never tried before.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Smith, Micholas D.
Sent: Thursday, December 10, 2015 9:32 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] constraining secondary structure gmx 5

Hi,

I haven't tried to restrain secondary structure; however, it may be possible by using a combination of dihedral, angle, and distance restraints (see section 4.3 in the manual). If you look up the DSSP . It would likely be cumbersome, but it may be do-able. The question is if the results from your simulation would be meaningful after all of these restraints were added. Perhaps it would be useful to see if you can build your system using OPLS or Amber instead of CHARMM and determine if the peptide's structure still "falls-apart".

Good Luck

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Yoav Atsmon-Raz <yoav.atsmonraz at ucalgary.ca>
Sent: Thursday, December 10, 2015 11:03 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] constraining secondary structure gmx 5

I've been trying to run a gromacs simulation of alternating d/l cyclical peptides (yes I know this is a dead horse that's been beat one time to many...) and after a lot of experimentation I managed to get an initial setup working via charmm gui. However, as the simulation progresses the structure becomes completely unstable which doesn't fit the experimental results that I'm familiar with in the literature. I was wondering if there is any way to manually constrain a secondary structure on a per residue basis beyond the definitions in the posre file. The reason I'm asking this is that I'm aware that this is possible in CHARMM and NAMD but I can't seem to find anything detailing this in the gromacs manual.

Thanks to anyone responding to this!
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