[gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2

Fri Nov 5 13:44:57 CET 2010

Hi,

all this has now been fixed I hope. The residues that I had missed are the ones my scripts not directly parse from the CHARMM ff files, i.e. they are hardcoded and hence I forgot to update the charge groups on them. Berk has now added an option of -1 to atoms added to terminals so that they become single charge groups as well, so that should be fine also. Let me know if I forgot something.

Regards,
Pär Bjelkmar

> Message: 2
> Date: Wed, 3 Nov 2010 20:10:08 +0000
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> Subject: Re: [gmx-users] Single atom charge group implementation for
> 	CHARMM27	in 4.5.2
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CD1C1A0.4060307 at soton.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Berk,
> 
> Thanks for the information, I just wanted to make sure that my message 
> had not been missed.
> 
> Cheers
> 
> Tom
> 
> On 03/11/10 19:37, Berk Hess wrote:
>> I forgot to say that for the water models the rtp entries are only 
>> used to recognize
>> the atoms. For the topology the itp files in the .ff dir are used.
>> 
>> Berk
>> 
>> ------------------------------------------------------------------------
>> From: gmx3 at hotmail.com
>> To: gmx-users at gromacs.org
>> Subject: RE: [gmx-users] Single atom charge group implementation for 
>> CHARMM27 in 4.5.2
>> Date: Wed, 3 Nov 2010 20:32:58 +0100
>> 
>> 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.piggot at soton.ac.uk
>>> To: gmx-users at 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 at 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-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> -- gmx-users mailing list gmx-users at 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-request at gromacs.org. Can't post? 
>> Read http://www.gromacs.org/Support/Mailing_Lists 
> 
> -- 
> Dr Thomas Piggot
> University of Southampton, UK.
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101103/1772b047/attachment.html
> 
> ------------------------------
> 
> -- 
> gmx-users mailing list
> gmx-users at 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!
> 
> End of gmx-users Digest, Vol 79, Issue 21
> *****************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101105/9e6cb3bb/attachment.html>