Re: [gmx-users] gmx hbond - specify precise atom names involved

Hi, Not as of yet I’m afraid. Erik > On 3 May 2016, at 08:16, Nash, Anthony wrote: > > > Hi all, > > Can gmx hbond accept user specified atoms for the donors (default OH and > NH) and acceptor (default O and N)? I don¹t seem to find any mention of > this in the -help text.

Re: [gmx-users] gmx hbond - specify precise atom names involved

On 5/3/16 5:21 PM, Nash, Anthony wrote: Thanks Justin, I’ll give that a try. I assume this approach would still require the .trr to be converted to a .gro file, and then the customised names ‘search-replaced’ with the respective ‘fake’ names? No. Names are read from the reference

Re: [gmx-users] gmx hbond - specify precise atom names involved

Thanks Justin, I’ll give that a try. I assume this approach would still require the .trr to be converted to a .gro file, and then the customised names ‘search-replaced’ with the respective ‘fake’ names? Thanks Anthony On 03/05/2016 16:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] gmx hbond - specify precise atom names involved

On 5/3/16 9:16 AM, Nash, Anthony wrote: Hi all, Can gmx hbond accept user specified atoms for the donors (default OH and NH) and acceptor (default O and N)? I don¹t seem to find any mention of this in the -help text. It's hard-coded in the source, so it's rather inflexible. I have a

[gmx-users] gmx hbond - specify precise atom names involved

Hi all, Can gmx hbond accept user specified atoms for the donors (default OH and NH) and acceptor (default O and N)? I don¹t seem to find any mention of this in the -help text. I have a post-trans modified protein from a rather bulk cross-linked peptide chain. I defined unique atom times but I