[gmx-users] Re:gmx-users Digest, Vol 54, Issue 23
Hi Justin, Thanks so much for your prompt response. If using AMBER force field, can one construct the parameters of non-standard molecules through ANTECHAMBER in AMBER package? Thanks in advance. Have a nice day. --- Jeffrey Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul Subject: Re: [gmx-users] some questions about gromacs To: Discussion list for GROMACS users Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed dcip1101 wrote: Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions carefully. 2. How to prepare parameters for a cofactor not included in the standard force fields? This is a very advanced topic. See here: http://wiki.gromacs.org/index.php/Parameterization 3. Any further suggestions to a new user to use the package better? Depends on what you are doing. Read lots of tutorials and consult the mailing list archive and wiki site (wiki.gromacs.org) if you have problems or are not certain how to implement certain features. -Justin Thanks so much for your time. Have a nice day. Jeffrey [EMAIL PROTECTED] 写道： Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.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. some questions about gromacs (dcip1101) 2. RE: Heat Flux and Lambda (Berk Hess) 3. Re: some questions about gromacs (Justin A. Lemkul) 4. Re: Pull.pdo Columns (Thomas Schlesier) 5. Re: steady (Justin A. Lemkul) 6. questions about using GROMACS (dcip1101) -- Message: 1 Date: Mon, 6 Oct 2008 17:52:45 +0800 (CST) From: dcip1101 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081006/6a76ccd9/attachment-0001.html -- Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Message: 4 Date: Mon, 6 Oct 2008
Re: [gmx-users] Re:gmx-users Digest, Vol 54, Issue 23
dcip1101 wrote: Hi Justin, Thanks so much for your prompt response. If using AMBER force field, can one construct the parameters of non-standard molecules through ANTECHAMBER in AMBER package? Yes. The parameter files can then be converted to Gromacs format using scripts present in the User Contributions section of the Gromacs website. -Justin Thanks in advance. Have a nice day. --- Jeffrey Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul Subject: Re: [gmx-users] some questions about gromacs To: Discussion list for GROMACS users Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed dcip1101 wrote: Dear all, I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers. 1. Can one use amber force field in gromacs? Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions carefully. 2. How to prepare parameters for a cofactor not included in the standard force fields? This is a very advanced topic. See here: http://wiki.gromacs.org/index.php/Parameterization 3. Any further suggestions to a new user to use the package better? Depends on what you are doing. Read lots of tutorials and consult the mailing list archive and wiki site (wiki.gromacs.org) if you have problems or are not certain how to implement certain features. -Justin Thanks so much for your time. Have a nice day. Jeffrey [EMAIL PROTECTED] 写道： Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.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. some questions about gromacs (dcip1101) 2. RE: Heat Flux and Lambda (Berk Hess) 3. Re: some questions about gromacs (Justin A. Lemkul) 4. Re: Pull.pdo Columns (Thomas Schlesier) 5. Re: steady (Justin A. Lemkul) 6. questions about using GROMACS (dcip1101) -- Message: 1 Date: Mon, 6 Oct 2008 17:52:45 +0800 (CST) From: dcip1101 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20081006/6a76ccd9/attachment-0001.html -- Message: 3 Date: Mon, 06 Oct 2008 07:03:58 -0400 From: Justin A. Lemkul ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu
