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.lars...@sbc.su.se>
Subject: Re: [gmx-users] GB Parameters
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <21e19e54-404f-42d2-8ddc-0684c6bb9...@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.lars...@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 <plo...@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
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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------------------------------
Message: 2
Date: Mon, 23 Aug 2010 13:01:45 -0700 (PDT)
From: "Bruce D. Ray" <bruced...@yahoo.com>
Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
[Justin]
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <508235.43845...@web35802.mail.mud.yahoo.com>
Content-Type: text/plain; charset="us-ascii"
On Mon, August 23, 2010 12:12 PM, Eudes Fileti <fil...@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 <fil...@ufabc.edu.br>
Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force
field [Mark, Justin]
To: gmx-users@gromacs.org
Message-ID:
<aanlkti=wzpazofhqpgngl1xe8ygrca2wfo_dxf_be...@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.abra...@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@gromacs.org>
Message-ID: <fbe4f0b22984.4c73c...@anu.edu.au>
Content-Type: text/plain; charset="us-ascii"
----- Original Message -----
From: fang yuan <fangyuan3...@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@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 <alanwil...@gmail.com>
Subject: [gmx-users] gmx 4.5 and openmm on Mac, still not compiling
To: Gromacs <gmx-users@gromacs.org>
Message-ID:
<aanlktikur=sw9jmbl97ltikrysxer9lmcya5mjlou...@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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