Re: [gmx-users] Regarding Residue in chain has different type (Other) from starting residue

Thank you Justin Sir, 1] But how do i solve this issue..?? and make sure that pdb2gmx is not interpreting my input as being a single chain and it's finding dissimilar residue types..?? even i tried with gmx pdb2gmx with -ter command, but still, i am getting the same results 2] If i view the

[gmx-users] grompp error

Dear Gromacs users, I got the following error when I tried to run grompp. ERROR 1 [file system.top, line 18]: ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I increased the box size and re-tried to run grompp,but it didn't

Re: [gmx-users] Regarding Residue in chain has different type (Other) from starting residue

On 10/15/17 2:42 AM, Dilip H N wrote: Hello, I have a simulations system and by gmx pdb2gmx i am generating the topology, but i am getting the warnings as:- Identified residue GLY1 as a starting terminus. Warning: Residue TMAO12 in chain has different type (Other) from starting residue GLY1

Re: [gmx-users] Running no periodic boundary condition simulation in GROMACS

Hi, See e.g. http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy but I think that as you have phrased it, your objective may not help find out anything useful. Mark On Sun, Oct 15, 2017 at 12:32 PM sanjeet kumar singh ch16d012 < ch16d...@smail.iitm.ac.in> wrote: > Dear all, >

[gmx-users] Running no periodic boundary condition simulation in GROMACS

Dear all, I want to run no pbc simulation for a single chain in GROMACS inorder to find out the forcefield applied potential energy of the chain. Can anyone please tell me how to do it? Thanks in advance -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Two questions about PME-User in coulombtype

Hi GMX Users, I'm using tabulized potentials between energygrp-table = Protein Ligand. I'm writing to inquiring the details of PME-User parameter. I have seen some discussions in the GMX User mail list and the explanation in user guide. I still can't ensure I have grasped the meaning of

[gmx-users] Regarding Residue in chain has different type (Other) from starting residue

Hello, I have a simulations system and by gmx pdb2gmx i am generating the topology, but i am getting the warnings as:- Identified residue GLY1 as a starting terminus. Warning: Residue TMAO12 in chain has different type (Other) from starting residue GLY1 (Protein). Warning: Residue TMAO13 in chain