Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hi Sourav, For Martini there's the conversion script martinize, which has an option -nt to suppress putting charges on termini. This is not really a Gromacs question, and it's better to post Martini related questions on the forum at http://cgmartini.nl Cheers, Tsjerk On May 24, 2016 23:35,

[gmx-users] Simulating conjugated protein

Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle, where my peptide is conjugated to a organic compound at the N terminal. The SDS micelle was genrated using CHARMM-GUI, here I am stuck with a problem for adding atom types for the compound. I tried adding atomtypes for

Re: [gmx-users] Combining various Flat-bottomed Potentials

Hi I am also interested in the issue of using a flat-bottomed restraint, for a spherocylinder. However, I am not sure whether the current gromacs settings of even a linear combination of a sphere and cylinder can help here to generate a spherocylinder. If we put the spherical and cylindrical

Re: [gmx-users] Combining various Flat-bottomed Potentials

Hi I am also interested in the issue of using a flat-bottomed restraint, for a spherocylinder. However, I am not sure whether the current gromacs settings of even a linear combination of a sphere and cylinder can help here to generate a spherocylinder. If we put the spherical and cylindrical

[gmx-users] ffbonded.itp

​Hi I want to simulate a glycoprotein, I have defined a new residue with charmm36 I should define some angles, bonds and dihedrals for this new residue in ffbonded.itp file, also in the ffbonded.itp file there is some other numbers and etc I dont know what are these and how to define correctly

[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of nodes. However, i am not clear on how to

[gmx-users] SAS for membrane protein

Hi dear gromacs users, It's the first time I use this mail list, I hope it will work fine. I have simulated a membrane protein in a lipid bilayer with water etc. Everything is fine but I now want to calculate the accessible surface of the protein. Can you help me to understand how does it work

Re: [gmx-users] SAS for membrane protein

On 5/24/16 8:43 AM, Maximilien LOPES RODRIGUES wrote: Hi dear gromacs users, It's the first time I use this mail list, I hope it will work fine. I have simulated a membrane protein in a lipid bilayer with water etc. Everything is fine but I now want to calculate the accessible surface of

[gmx-users] Deprotonated Asp and Glu

Hello I have simulated a protein ligand complex and analyzed the trajectory. After visualization of time frames and clusters.pdb; It occurs to me that the Asp and Glu are nit deprotonated although during pdb2gmx I used -inter command and deprotonated both residue according to pH 7. Can anyone

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

On 5/23/16 5:31 AM, zeineb SI CHAIB wrote: I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's: WARNING: atom HA is missing in residue HEM 473 in the pdb file You

Re: [gmx-users] Deprotonated Asp and Glu

Allright Thank you very much for quick response. Sent from my iPhone > On 24-May-2016, at 6:05 pm, "Smith, Micholas D." wrote: > > Best thing to do would be to check the *.gro and *.top files and see if it > really is deprotonated. > > === > Micholas Dean

Re: [gmx-users] ?==?utf-8?q? SAS for membrane protein

> The calculation group is protein + membrane, then choose just the protein for > output. > > -Justin Hi Justin, thanks for replying so fast. So I have to create a group protein + membrane using index.ndx but I don't understand how to output the protein only. With the command gmx sasa, I just

Re: [gmx-users] Deprotonated Asp and Glu

The charge on Asp amd Glu seems 0 and hydrogens are present in time frames and cluster.pdb. But I deprotonated during pd2gmx. Sent from my iPhone > On 24-May-2016, at 6:00 pm, sun wrote: > > Hello > I have simulated a protein ligand complex and analyzed the trajectory.

Re: [gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

On 5/24/16 6:35 AM, Antara mazumdar wrote: Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of

Re: [gmx-users] Deprotonated Asp and Glu

On 5/24/16 8:30 AM, sun wrote: Hello I have simulated a protein ligand complex and analyzed the trajectory. After visualization of time frames and clusters.pdb; It occurs to me that the Asp and Glu are nit deprotonated although during pdb2gmx I used -inter command and deprotonated both residue

Re: [gmx-users] ffbonded.itp

On 5/24/16 6:20 AM, a.om...@shirazu.ac.ir wrote: ​Hi I want to simulate a glycoprotein, I have defined a new residue with charmm36 I should define some angles, bonds and dihedrals for this new residue in ffbonded.itp file, also in the ffbonded.itp file there is some other numbers and etc I

Re: [gmx-users] Deprotonated Asp and Glu

Best thing to do would be to check the *.gro and *.top files and see if it really is deprotonated. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

Re: [gmx-users] angle_restraint_z

On 5/24/16 10:36 AM, Karina wrote: Hello, I am trying to restrain the angle between two atoms (type a5) in a half spherical body with respect to the z axis. I am trying to use angle_restraint_z, but not sure how to do it correctly due to lack of information in the manual or in forums. I have

Re: [gmx-users] small molecule aggregation analysis

On 5/24/16 12:19 PM, Surahit Chewle wrote: Hello Everyone, I have simulated a system of 10 synthetic drug molecules (each 20 atoms) in small organic solvent, methanol on Gromacs 4.6.5 as far as I have read, there are many tools available for protein aggregation, but if you can suggest a tool

Re: [gmx-users] Combining various Flat-bottomed Potentials

On 5/24/16 12:30 PM, Christopher Neale wrote: I doubt it. The flat-bottom potential in the pull-code is not really the standard definition of a flat-bottom potential. In my opinion, a flat-bottom potential has a low, and a high defined value and then the restraint increases harmonically

[gmx-users] small molecule aggregation analysis

Hello Everyone, I have simulated a system of 10 synthetic drug molecules (each 20 atoms) in small organic solvent, methanol on Gromacs 4.6.5 as far as I have read, there are many tools available for protein aggregation, but if you can suggest a tool of choice for small molecule aggregation, for

Re: [gmx-users] Combining various Flat-bottomed Potentials

I doubt it. The flat-bottom potential in the pull-code is not really the standard definition of a flat-bottom potential. In my opinion, a flat-bottom potential has a low, and a high defined value and then the restraint increases harmonically above high and below low with no penalty between low

Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

Dear Teemu: Thank you for the help. After a but of fiddling your suggestion did lead to the solution: echo -e "\"group_&_1\"\n\"group_&_2\" | gmx ... Is this really what you had in mind? If so, I think I'll still submit a feature request since I doubt we can expect all users to come up with

Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

Hi, On Tue, May 24, 2016 at 8:22 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Thank you for the help. After a but of fiddling your suggestion did lead > to the solution: > > echo -e "\"group_&_1\"\n\"group_&_2\" | gmx ... > > Is this really what you had in mind? That will

[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hello I am trying to put selective charges on the termini, I am getting stuck at the initial stage where I am supposed to mention the force-field needed. As martini termini differ from conventional ones, I am unable to bypass NH3+ or COO- termini options at the start and end respectively as there

[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hello I am trying to put selective charges on the termini, I am getting stuck at the initial stage where I am supposed to mention the force-field needed. As martini termini differ from conventional ones, I am unable to bypass NH3+ or COO- termini options at the start and end respectively as there

Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

On 5/24/16 5:33 PM, Sourav Ray wrote: Hello Thanks for your answer, I presume pdb2gmx needs some force-field definitions to work, anyway, can I assign charges selectively to certain atom number? Let me know if it is feasible, I searched the forums but couldn't find anything specific. Try

Re: [gmx-users] Combining various Flat-bottomed Potentials

Thanks for the clarification Justin. Those interested in using these potentials (as I was) should be careful as I think that at lease some forms are broken when using domain decomposition: http://redmine.gromacs.org/issues/1969 From:

Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hello Thanks for your answer, I presume pdb2gmx needs some force-field definitions to work, anyway, can I assign charges selectively to certain atom number? Let me know if it is feasible, I searched the forums but couldn't find anything specific. Regards Sourav On Wed, May 25, 2016 at 2:48 AM,

Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hi, If you've already arranged your own termini, then you can choose "None" from the options pdb2gmx presents. Mark On Tue, May 24, 2016 at 11:15 PM Sourav Ray wrote: > Hello > > I am trying to put selective charges on the termini, I am getting stuck at > the initial

[gmx-users] Release of FESetup 1.2

Hello everyone, we are delighted to announce the release of FESetup 1.2. FESetup is a tool to automate the setup of (relative) alchemical free energy simulations like thermodynamic integration (TI) and free energy perturbation (FEP) as well as post–processing methods like MM–PBSA and LIE.