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: [email protected] To: [email protected] Sent: Tuesday, August 24, 2010 2:51:14 AM Subject: gmx-users Digest, Vol 76, Issue 120 Send gmx-users mailing list submissions to [email protected] 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 [email protected] You can reach the person managing the list at [email protected] 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 <[email protected]> Subject: Re: [gmx-users] GB Parameters To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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 <[email protected]>: > 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 <[email protected]>: > >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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" <[email protected]> Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin] To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" On Mon, August 23, 2010 12:12 PM, Eudes Fileti <[email protected]> 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 <[email protected]> Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark, Justin] To: [email protected] Message-ID: <[email protected]> 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 <[email protected]> Subject: Re: [gmx-users] Does anyone know how to get the file charmm_gromacs.tar.gz? To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" ----- Original Message ----- From: fang yuan <[email protected]> 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 <[email protected]> > 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 <[email protected]> Subject: [gmx-users] gmx 4.5 and openmm on Mac, still not compiling To: Gromacs <[email protected]> Message-ID: <[email protected]> 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 [email protected] 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 [email protected] 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 [email protected]. Can't post? 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