Re: [gmx-users] Using specbond.dat in pdb2gmx

On 6/16/14, 12:31 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still fin

Re: [gmx-users] Using specbond.dat in pdb2gmx

Dr. Justin Lemkul, >> Ah I see. I also noticed that in the original specbond.dat, the bond >> distance specification for the disulfide bonds between 2 CYS's or between 2 >> CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I >> still find a bit unclear is the final columns

Re: [gmx-users] g_cluster for ligand clustering

On Sat, Jun 14, 2014 at 5:18 PM, wrote: > Dear all, > > I have a trajectory file of a protein+ligand binding simulation. > What I would like to do is to cluster the ligands positions from the > simulation trajectory. But although I have tried quite a few possibilities, > the RMSD calculation usin

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Hi Sucharita, Please post as new thread or in g_mmpbsa forum. You could install Gromacs at new location using followings with cmake: -DCMAKE_INSTALL_PREFIX=/to/custom/path -DBUILD_SHARED_LIBS=OFF -DGMX_GPU=off Then, g_mmpbsa can be compiled using this Gromacs. We will fix this installation issu

Re: [gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc

On 6/16/14, 9:05 AM, Saman Shahriyari wrote: dear users I have an .xtc file regarding an interacting protein/peptide complex. as i extract a pdb from this trajectory, i find the peptide separated from protein and in a position very far from it. i derived a pdb from .tpr file, to make sure that

[gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc

dear users I have an .xtc file regarding an interacting protein/peptide complex. as i extract a pdb from this trajectory, i find the peptide separated from protein and in a position very far from it. i derived a pdb from .tpr file, to make sure that my starting structure is intact compared to th

Re: [gmx-users] How to extend Amber FF parameters of Lipids

On 6/16/14, 6:47 AM, Batdorj Batsaikhan wrote: Dear gmx users, I would like to simulate lipid with a protein using AMBER force field. Have you any advice and useful links? http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2 -Justin -- ==

Re: [gmx-users] Regarding lipid topology

Of course, no. You need to adjust your topology (force field?) to distinguish between cis- and trans- states. Dr. Vitaly V. Chaban On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy wrote: > Dear all, > I want to simulate a membrane protein system. My membrane is composed of > DOPC (cis isomer) an

[gmx-users] How to extend Amber FF parameters of Lipids

Dear gmx users,  I would like to simulate lipid with a protein using AMBER force field. Have you any advice and useful links? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

[gmx-users] Regarding lipid topology

Dear all, I want to simulate a membrane protein system. My membrane is composed of DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology from lipidbook website. Since DOPC and DEPC are isomers, can I use the topology of DOPC for DEPC also? Thank and regards Venkat Reddy Chira