Re: [gmx-users] Serine phosphorylation

http://vienna-ptm.univie.ac.at/ On Mon, Jan 11, 2016 at 11:11 PM, Simone Bolognini wrote: > Thank you! Putting every hint together made the thing work perfectly! Now, > I would be interested in performing some trial simulations in implicit > solvent. However, GROMACS

Re: [gmx-users] How to fix miising atoms in a pdb file?

For what I know, if you open the pdb file with SPDBV il will automatically fix the missing atoms. Then you should only take care of saving the new structure in a new pdb and you're done! Simone Il 13/gen/2016 08:13, "Seera Suryanarayana" ha scritto: > Dear gromacs users, >

[gmx-users] Installation of two versions of Gromacs on one system

Good afternoon sir/ma'am, I am using Gromacs-4.6.5 on my system (Ubuntu14.04LTS). I want to install Gromacs-4.5.6 on the same system. I have tried to install it as tutorial available on Gromcas site, but after sudo make install command, when I tried to run commands: g_rms_mod It give error:

[gmx-users] How to fix miising atoms in a pdb file?

Dear gromacs users, I have one pdb file which does not have one atom and I need to be fixed that atom in the pdb to run MD simulations. Kindly suggest me to how to fix it. Can I mutate the residue of my interest with the same residue by using pymol or SPDBV to fix the missing atoms? Thanks in

[gmx-users] planarity restrain for ligand

Dear Gromacs users, I am running an energy minimization on a protein ligand complex. The ligand is a nucleotide and after the em the base loses its planarity. I will be grateful if you let me know if a non-planar base is physically possible or not. If not, what procedure i have to follow to

Re: [gmx-users] How to delete Zinc atom from .xtc and .gro files

On 1/12/16 9:32 AM, Hassan Aaryapour wrote: Dear Gromacs Users, How can I remove Zinc atoms from .xtc and .gro files after MD simulation. Use trjconv with a suitable index group containing only the atoms you want to keep. -Justin -- ==

[gmx-users] Non-Integral Charges

Hello Everyone I want to know how to change the non-integral charges? I am simulating a pentameric model of protein in water and the net charge comes out to be -5.0. Everything goes ok till final mdrun. As soon as its started, it carshes. Is it dus to wring topology as the charges are

Re: [gmx-users] Non-Integral Charges

On 1/12/16 8:54 AM, sun wrote: Hello Everyone I want to know how to change the non-integral charges? I am simulating a pentameric model of protein in water and the net charge comes out to be -5.0. Everything goes ok till final mdrun. As soon as its started, it carshes. Is it dus to wring

[gmx-users] How to delete Zinc atom from .xtc and .gro files

Dear Gromacs Users, How can I remove Zinc atoms from .xtc and .gro files after MD simulation. Thanks Hassan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] planarity restrain for ligand

On 1/12/16 8:10 AM, ansu...@physics.iisc.ernet.in wrote: Dear Gromacs users, I am running an energy minimization on a protein ligand complex. The ligand is a nucleotide and after the em the base loses its planarity. I will be grateful if you let me know if a non-planar base is physically

Re: [gmx-users] viscosity using green kubo relation for ionic liquids

I tried with g_energy -vis , but it calculates using einstein relation. I want to calculate using green kubo equation. regards, shanu On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel wrote: > On 11/01/16 22:54, shanmuga sundaram wrote: > >> Hello all, >> >> >> I am

Re: [gmx-users] viscosity using green kubo relation for ionic liquids

EqMD methods work poorly for highly and moderate viscous liquids. On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram wrote: > I tried with g_energy -vis , but it calculates using einstein relation. I > want to calculate using green kubo equation. > > > regards, > >

Re: [gmx-users] g-membed +KALP in dppc

On 1/12/16 3:13 PM, ‪neda razavi‬ ‪ wrote: dear admins i read in kalp in dppc tutorial that we should define an strong position restrain for protein in order to use inflateGRO. I wonder to know whether we should use this strong position restraint for protein when using g_membed or not?

Re: [gmx-users] genion with Na or Ca

Ca(2+) will block one of your binding sites, if you care. On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak wrote: > Hi all, > > > I have a quick question about neutralizing the system. I have a solvated > system that contains a charged protein of -2q. Is there a

Re: [gmx-users] genion with Na or Ca

At low concentrations (just a single Ca2+) you shouldn't expect any huge differences, though the Ca2+ may stick around the protein surface a little bit longer than the Na+ ions which may alter how one of the charged residues is hydrated. If the protein is of a modest size (not a small

Re: [gmx-users] genion with Na or Ca

On 1/12/16 3:19 AM, Turgay Cakmak wrote: Hi all, I have a quick question about neutralizing the system. I have a solvated system that contains a charged protein of -2q. Is there a major difference betwen adding 2 Na ions and a single Ca ion to neutralize the system (using genion)? For

[gmx-users] g-membed +KALP in dppc

dear admins i read in kalp in dppc tutorial that we should define an strong position restrain for protein in order to use inflateGRO. I wonder to know  whether we should use this strong position restraint for protein when using g_membed or not? -- Gromacs Users mailing list * Please search the