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 ----- > From: gmx-users-requ...@gromacs.org > To: gmx-users@gromacs.org > Sent: Tuesday, August 24, 2010 2:51:14 AM > Subject: gmx-users Digest, Vol 76, Issue 120 > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> -- >> 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/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/mailing_lists/users.php > > > ------------------------------ > > 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 > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/6f3c3cc1/attachment-0001.html > > ------------------------------ > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100823/b56e3650/attachment-0001.html > > ------------------------------ > > 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100824/0acc23bf/attachment-0001.html > > ------------------------------ > > 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<< > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100824/79afbe3e/attachment.html > > ------------------------------ > > -- > 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/search before posting! > > End of gmx-users Digest, Vol 76, Issue 120 > ****************************************** > -- > 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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
