[gmx-users] GB Parameters

Per Larsson per.larsson at sbc.su.se
Tue Aug 24 14:36:03 CEST 2010 

Hi!

You are correct, expect that the values in column 4 (the Vdw-radii for atom types) that are being used to calculate the Born radii currently are force field and radii-algorithm agnostic (as is indeed the case in Tinker as well).
Obviously, if someone wants to use other Vdw-radii, such as eg. the Bondi, these values will need to be changed.

Good luck!
/Per

24 aug 2010 kl. 13.05 skrev Elizabeth Ploetz:

> Greetings!  
> 
> Thank you both for such timely and helpful responses.  Below I have listed how I (and anyone interested in using their own force field) should modify the gbsa.itp file, according to my new understanding.  Please let me know if I am wrong.
> 
> Columns 1-3:  Leave them alone, they are not used in 4.5beta3
> Column 4:     Use the force field's LJ sigma/2 (except for hydrogen: use 0.115 regardless of the hydrogen's sigma value)
> Column 5:     Leave it as is, because the HCT scaling factors are not force field specific
> 
> Prof. van der Spoel, unfortunately our force field does not support nucleic acids either.  Per, I will let you know if I find any errors, however I am new to implicit solvent methods, so I have a lot of learning to do first!  
> 
> Best, 
> 
> E. A. Ploetz
> 
> ----- Original Message -----
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> Today's Topics:
> 
>   1. Re: GB Parameters (Per Larsson)
>   2. Re: Charmm to Gromacs: Polyols force field [Justin] (Bruce D. Ray)
>   3. Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force
>      field [Mark,	Justin] (Eudes Fileti)
>   4. Re: Does anyone know how to get the file
>      charmm_gromacs.tar.gz? (Mark Abraham)
>   5. gmx 4.5 and openmm on Mac, still not compiling (Alan)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 23 Aug 2010 20:41:51 +0200
> From: Per Larsson <per.larsson at sbc.su.se>
> Subject: Re: [gmx-users] GB Parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <21E19E54-404F-42D2-8DDC-0684C6BB9421 at sbc.su.se>
> Content-Type: text/plain;	charset=us-ascii
> 
> Also, again, as David said, if you find any errors in the parameters or in the code, please let me know!
> 
> Cheers
> /Per
> 
> 
> 23 aug 2010 kl. 20:09 skrev Per Larsson <per.larsson at sbc.su.se>:
> 
>> Hi!
>> 
>> Values in columns 1-3 are not currently used in version beta3. They pertain to more elaborate surface area algorithms, the one from Still et al in particular.
>> 
>> Column 4 is the Vdw-radii for atom types that are used for computing the Born radii. The dielectric offset is specified in the mdp-file, and gets added to the input radii for the different radii methods.
>> 
>> Column 5 is the scale factor for the HCT/OBC models. The values are taken from the original HCT reference, as well as the corresponding implementation in Tinker. 
>> 
>> /Per
>> 
>> 23 aug 2010 kl. 19:27 skrev Elizabeth Ploetz <ploetz at ksu.edu>:
>> 
>>> Dear Gromacs Users, 
>>> 
>>> I am interested in implementing implicit solvent using the OBC GBSA method.  In the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple versions of amber) contain the gbsa.itp file, and one (charmm27), contains a gb.itp file.  They all have the same column titles (sar, st, pi, gbr, and hct).  I have read the six articles listed at http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent, however I still have the following two questions regarding the contents of this file:
>>> 
>>> (1.)  What values are tabulated in these columns and what are the corresponding references for each of them?
>>> (2.)  Which columns are used (versus ignored) by Gromacs in the implementation of each of the methods (Still/HCT/OBC)?
>>> 
>>> Here are my guesses for Question 1:
>>> (a.)  sar: solvent accessible surface area?
>>> (b.)  st: surface tension?
>>> (c.)  pi: ?
>>> (d.)  gbr: generalized born radius?  These values correspond to sigma/2 from Jorgensen and Tirado-Rives' 1988 JACS paper (v. 110, p. 1657).  However the generalized born radius is equal to Rvdw plus a dielectric offset distance, according to Still et al's 1997 J. Phys. Chem. A paper (v. 101, p. 3005).  This would mean the dielectric offset distance is set to zero (?).  
>>> (e.)  hct: HCT parameter
>>> 
>>> With an eventual goal of implementing implicit solvent using my lab's force field, insight into the meaning of the columns and/or references for their origin would be greatly appreciated. 
>>> 
>>> Thanks in advance! 
>>> 
>>> Sincerely yours,
>>> 
>>> E. A. Ploetz
>>> -- 
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> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 23 Aug 2010 13:01:45 -0700 (PDT)
> From: "Bruce D. Ray" <brucedray at yahoo.com>
> Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
> 	[Justin]
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <508235.43845.qm at web35802.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> On Mon, August 23, 2010 12:12 PM, Eudes Fileti <fileti at ufabc.edu.br> wrote:
> 
>> Well, the line 40 is just one of the 36 parameters not found!
>> In this link ( https://sites.google.com/site/fileti/ ) I put
>> the complete files. 
>> I know I need to determine which bond type should be called
>> and I believe that it has been done, but I don't know why
>> it's not being found.
> 
> Well, I'm not Justin, but as I look at your topology, I see
> that you have a bond from atom 3, type CC322, to atom 6,
> also type CC322.  However, when I look at the parameters you
> give in the bondtypes section, I cannot find a CC322  CC322
> bond defined.  Either the entry is missing or you did not
> post a complete set of force field entries.
> 
> Missing entries might be the cause of theother parameters
> not found as well, which is what was suggested to you
> previously.
> 
> 
> -- 
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN  46202-3273
> 
> 
> 
> 
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> ------------------------------
> 
> Message: 3
> Date: Mon, 23 Aug 2010 17:46:20 -0300
> From: Eudes Fileti <fileti at ufabc.edu.br>
> Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force
> 	field [Mark,	Justin]
> To: gmx-users at gromacs.org
> Message-ID:
> 	<AANLkTi=WZPAZofhqpgnGL1XE8yGRca2WfO_Dxf_Bepuj at mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
> 
> Ol�,
> Mark and Justin.
> Solved.
> I did what you suggested and I got all the default values.
> 
> Muito obrigado!
> eef
> 
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ci�ncias Naturais e Humanas
> Universidade Federal do ABC � CCNH
> Av. dos Estados, 5001
> Santo Andr� - SP - Brasil
> CEP 09210-971
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
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> ------------------------------
> 
> Message: 4
> Date: Tue, 24 Aug 2010 13:09:55 +1000
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] Does anyone know how to get the file
> 	charmm_gromacs.tar.gz?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbe4f0b22984.4c73c4a3 at anu.edu.au>
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> 
> ----- Original Message -----
> From: fang yuan <fangyuan3623 at gmail.com>
> Date: Tuesday, August 24, 2010 4:52
> Subject: Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
>> Hi, I have the same problem, I need to implement the general CHARMM forcefield in gromacs, so I need to know how to convert the rtf files into rtp files in gromacs
> 
> There's never been an automated tool for that.
> 
> Mark
> 
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> ------------------------------
> 
> Message: 5
> Date: Tue, 24 Aug 2010 08:49:38 +0100
> From: Alan <alanwilter at gmail.com>
> Subject: [gmx-users] gmx 4.5 and openmm on Mac, still not compiling
> To: Gromacs <gmx-users at gromacs.org>
> Message-ID:
> 	<AANLkTikur=SW9jMbL97LtikrYSxer9LMcYa5MjLOuzva at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi there,
> 
> I've tried before and the error still basically the same (line error in
> 'nb_kernel400_x86_64_sse.c' was 630, now's 629) .
> 
> I am using gmx 4.5 release-4-5-patches branch.
> 
> git pull
> rm -fr build
> mkdir -p build
> cd build
> cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF ..
> make clean
> make -j 2
> sudo make install # all fine till here
> make clean
> export OPENMM_ROOT_DIR=/usr/local/openmm
> cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON ..
> make mdrun
> 
> [snip]
> [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o
> [ 56%] Building C object
> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:
> In function ���nb_kernel400nf_x86_64_sse���:
> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
> error: ���gmx_invsqrt_exptab��� undeclared (first use in this function)
> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
> error: (Each undeclared identifier is reported only once
> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
> error: for each function it appears in.)
> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
> error: ���gmx_invsqrt_fracttab��� undeclared (first use in this function)
> make[3]: ***
> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o]
> Error 1
> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
> 
> Any help would be appreciated.
> 
> Thanks,
> 
> Alan
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>> http://www.bio.cam.ac.uk/~awd28<<
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