Hi, I saw your message, but I wanted to discuss with others before answering. I have not had a chance for that yet, but I can answer anyhow.
1. This is a mistake. The person converting the original Charmm files edited his conversion script, but the "special cases" can not be treated with this script. We'll update them. 2. Water is always a special case. It charge group is smaller than most other charge groups and force field independent. For performance reasons we don't want to change this. (although in a future release we might get rid of the complete charge group concept) 3. Termini charge groups were also overlooked. We can fix this. I added support for charge group numbers in the tdb file some time ago. Berk > Date: Wed, 3 Nov 2010 14:50:34 +0000 > From: t.pig...@soton.ac.uk > To: gmx-users@gromacs.org > Subject: [gmx-users] Single atom charge group implementation for CHARMM27 in > 4.5.2 > > Hi, > > I sent this message a few days ago to the list but have not had a reply. > I feel some of the issues are quite important and so I am sending it again: > > > I have a few questions/comments about the implementation of the single > atom charge groups with the CHARMM27 force field that maybe someone can > help with: > > 1. There are some entries in aminoacids.rtp which have not been > converted to having every atom in a separate charge group (ASPP, CYS2, > GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I > understand these are some of the less commonly used entries, have they > been left out for a reason? By the way I also noticed during a quick > test for this that there is not an rtp entry for ARGN but it is given as > an option by pdb2gmx when using -inter. > > 2. Relating to 1 are the charge groups in the water models, which have > also been left as a water in a single charge group. I think I remember > reading somewhere that this is needed for the fast water loops in > GROMACS, so I assume this has been done on purpose. My concern is that > this is different to the TIP3P and TP3M entries in the aminoacids.rtp > file. If this has been done on purpose for the water models, then maybe > TIP3 and TP3M should also just have one charge group (as in the HOH entry)? > > 3. Finally, another concern I have is that when adding termini to a > protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal > atoms are still added as one charge group by pdb2gmx. I am not sure of a > way around this, apart from still using the -nochargegrp option, or > having AMBER forcefield style rtp entries for the N and C terminal > residues (undesirable I am sure). > > Cheers > > Tom > > On 30/10/10 20:56, Rossen Apostolov wrote: > > Dear Gromacs users and developers, > > > > A new bugfix release of Gromacs is now available: > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. > > > > Here is a list of some of the resolved issues for 4.5.1: > > > > * CHARMM force field now has single atom charge groups (pdb2gmx > > -nochargegrp no longer required) > > * Made pdb2gmx -chainsep option work > > * Fixed possible inconvenient npme node choice with pme load between 0.33 > > and 0.50 which could lead to very slow mdrun performance. > > * Made Generalized Born gb_algorithm and sa_surface_tension active and > > added a separate non-polar solvation term to the output. > > * Fixed issues in Generalized Born code that could cause incorrect results > > with SSE and all-vs-all inner-loops. > > * Fixed bug with pressure coupling with nstlist=-1 that resulted in > > extremely low densities. > > * Fixed corrupted energy and checkpoint file output with BAR free energy > > calculations. > > * Fixed normalization of g_density using only the last frame. > > * Fixed several issues with cmake > > * Several minor fixes. > > > > > > Once again big thanks to all developers for their hard work, and to all > > users for their contributions! > > > > Happy simulating! > > Rossen > > > > > > -- > Dr Thomas Piggot > University of Southampton, UK. > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
