Re: [gmx-users] atom indexing in top and gro files

Dear Justin, Many thanks for your quick reply! I really appreciate it. * The code requires all [moleculetype] directives to be numbered from 1. This has no relationship to the actual global atom numbers in the coordinate file. What must be true is that the atoms in the topology and

[gmx-users] atom indexing in top and gro files

Dear Colleague, I just wonder how exactly are the atom numbering in gro files and in the “atoms” section of topology files used. There does not seem to be much information on the file format manual pages. (i.e.

[gmx-users] GMXLIB for pdb2gmx

Hello colleagues, I would like to do experiments on a force field. Hence I cloned the force field files from shares/gromacs/top to a local directory, at $HOME/top. According to the manual page at http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html I need to set the

[gmx-users] searching this mailing list

Dear colleagues, Just wonder how can I search past discussions for keywords in this mailing list? I tried the search box on the top left of the Gromacs home page, but it does not seem to work. (Just try some keywords from the title of a discussion.) I may be missing something obvious … Ling

[gmx-users] pdb2gmx , or equivalent

I see, thank you Justin. Suppose you mean ASP vs ASH, HID, HIE, HIP, etc.? But how about disulfide bridges? Does pdb2gmx respect SSBOND and / or CONECT records in the PDB? Perhaps it will re-evaluate them regardless? Also, I see on the pdb2gmx manual page that the default glutamine is charged.

[gmx-users] pdb2gmx , or equivalent

the clean up stage. I see that one can either let the clean up happen automatically, or have you tell it interactively whenever there is a decision to make. I would just like it to respect my structure – in the sense that no hydrogen is added or removed. Thank you. Ling Chan Notice of Confidentiality