[gmx-users] Simulation of D-Alanine

Hi Group: I am trying to simulate a peptide containing D-Alanine (DAL). For this purpose, I am using Charmm36m Force Field. While running the command 'pdb2gmx -f input.pdb -ignh -ff charmm36-july17', I got an error saying 'DAL is not defined' (something similar to this). I understand that the

[gmx-users] 3-10 or Pi helices are changing to Alpha over the time: 100 ns MD

Hi Group I have been trying to run a simulation that contains both 3-10 and alpha helical peptides. I am using "AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)" forcefield. Over the course of simulation, the 3-10 helix is changing to alpha as

Re: [gmx-users] How to make a program run on the trajectory

; problem here... > > > > Therefore, could you please state more specifically what is it that you > > can't accomplish? Please be more verbose as well, it should help. > > > > Thank you, > > João > > > > On Fri, Sep 16, 2016 at 8:23 PM, prasu

[gmx-users] How to make a program run on the trajectory

Hello I have written some programs in Fortran and PERL. Now I want to make them run on a trajectory file (.trr). Can some body guide me for the same. I believe that it must be available on net. However, I was not able to find so. Thanx in advance. Regards Prasun PRASUN (ASHOKA) Desire +

[gmx-users] Adding missing heavy atoms

Dear All I have generated the base atoms of nucleotides in a structure, but it does not have sugar and phosphate atoms. Is there any method by which I can add them appropriately (either in A or B form) Thanx in advance PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work =

[gmx-users] Fwd: Implicit solvent simulation

Dear All I am planning to study the effect of adding the ions on the dodecamer protein. For this purpose I need to add ions (Fe2+) in the system. Any suggestion for it. I have come to know through various discussion forums that there is no need of adding ions to make the system neutral, but in

Re: [gmx-users] Fwd: Implicit solvent simulation

Lemkul jalem...@vt.edu wrote: On 2/10/14, 7:47 AM, prasun kumar wrote: Dear All I am planning to study the effect of adding the ions on the dodecamer protein. For this purpose I need to add ions (Fe2+) in the system. Any suggestion for it. I have come to know through various discussion

Re: [gmx-users] Fwd: Implicit solvent simulation

Lemkul jalem...@vt.edu wrote: On 2/10/14, 7:47 AM, prasun kumar wrote: Dear All I am planning to study the effect of adding the ions on the dodecamer protein. For this purpose I need to add ions (Fe2+) in the system. Any suggestion for it. I have come to know through various discussion