[gmx-users] first residue in chains warning issue

Dear all, I built a triple helix with 2 GLN and 1 SER being the first residue of the three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type for GLN-1 and SER-1, I came across the following

Re: [gmx-users] HYL force field

Hi, 范聪 I have never worked with ligand, and will try to learn this tutorial. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ?? Sent: Monday, 11 May 2015 11:03 AM To:

Re: [gmx-users] HYL force field

Hello, can you treat HYL as ligand and build its forcefield parameters referring to this link http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html At 2015-05-11 08:39:39, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I want to simulate a protein containing

[gmx-users] Sanjay (Re: Energy minimization problem)

HI,    I am running membrane protein dynamics. After energy minimization i am getting the following error. I am not getting how to rectify it.    Energy is minimized in fewer steps. Without proper minimization i cant proceed to next step of NVT run. Here is the error:  Steepest Descents: