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Hello, gods of gromacs,<br><br>I have ported the parmbsc0 modifications to a new gromacs force field, based on the amber99sb.ff, this involves adding a new carbon atom (CI) to be used in the C5' of nucleotides. <br><br>Everything is working perfectly (to my astonishment) and I am confident of all of the modifications I have made, except for the func column in [diheadraltypes]. The only way I can get the parameters that involve the same four atoms to work is to alter this column. I have read chapter 5 but I cannot see in what way this will affect the new ff.<br><br>These are the original parameters from AMBERparmbsc0:<br><br>DIHE<br>X -CI-OS-X 3 1.150 0.0 3.0<br>X -CI-OH-X 3 0.500 0.0 3.0<br>X -CI-CT-X 9 1.400 0.0 3.0<br>CT-OS-CT-CI 1 0.383 0.0 -3.0<br>CT-OS-CT-CI 1 0.100 180.0 2.0<br>H1-CI-CT-OS 1 0.250 0.0 1.0<br>H1-CI-CT-OH 1 0.250 0.0 1.0<br>H1-CT-CI-OS 1 0.250 0.0 1.0<br>H1-CT-CI-OH 1 0.250 0.0 1.0<br>CI-CT-CT-CT 1 0.180 0.0 -3.0<br>CI-CT-CT-CT 1 0.250 180.0 -2.0<br>CI-CT-CT-CT 1 0.200 180.0 1.0<br>OS-P -OS-CI 1 0.185181 31.79508 -1.0 alfa<br>OS-P -OS-CI 1 1.256531 351.95960 -2.0 alfa<br>OS-P -OS-CI 1 0.354858 357.24748 3.0 alfa<br>OH-P -OS-CI 1 0.185181 31.79508 -1.0 alfa<br>OH-P -OS-CI 1 1.256531 351.95960 -2.0 alfa<br>OH-P -OS-CI 1 0.354858 357.24748 3.0 alfa<br>CT-CT-CI-OS 1 1.178040 190.97653 -1.0 gamma<br>CT-CT-CI-OS 1 0.092102 295.63279 -2.0 gamma<br>CT-CT-CI-OS 1 0.962830 348.09535 3.0 gamma<br>CT-CT-CI-OH 1 1.178040 190.97653 -1.0 gamma<br>CT-CT-CI-OH 1 0.092102 295.63279 -2.0 gamma<br>CT-CT-CI-OH 1 0.962830 348.09535 3.0 gamma<br><br>This is from my amberbsc0/ffbonded.itp:<br>;i j k l func phase kd pn<br>CT OS CT CI 4 0.00 0.38300 -3 ; parmbsc0 ----> Will Stebbeds<br>CT OS CT CI 4 180.00 0.10000 2 ; parmbsc0 ----> Will Stebbeds<br>H1 CI CT OS 4 0.00 0.25000 1 ; parmbsc0 ----> Will Stebbeds<br>H1 CI CT OH 4 0.00 0.25000 1 ; parmbsc0 ----> Will Stebbeds<br>H1 CT CI OH 4 0.00 0.25000 1 ; parmbsc0 ----> Will Stebbeds<br>CI CT CT CT 4 0.00 0.18000 -3 ; parmbsc0 ----> Will Stebbeds<br>CI CT CT CT 4 180.00 0.25000 -2 ; parmbsc0 ----> Will Stebbeds<br>CI CT CT CT 4 180.00 0.20000 1 ; parmbsc0 ----> Will Stebbeds<br>OS P OS CI 4 31.79 0.18518 -1 ; parmbsc0 ----> Will Stebbeds<br>OS P OS CI 4 351.96 1.25653 -2 ; parmbsc0 ----> Will Stebbeds<br>OS P OS CI 4 357.25 0.35486 3 ; parmbsc0 ----> Will Stebbeds<br>OH P OS CI 4 31.79 0.18518 -1 ; parmbsc0 ----> Will Stebbeds<br>OH P OS CI 4 351.96 1.25653 -2 ; parmbsc0 ----> Will Stebbeds<br>OH P OS CI 4 357.25 0.35486 3 ; parmbsc0 ----> Will Stebbeds<br>CT CT CI OS 4 190.98 1.17804 -1 ; parmbsc0 ----> Will Stebbeds<br>CT CT CI OS 4 295.63 0.09210 -2 ; parmbsc0 ----> Will Stebbeds<br>CT CT CI OS 4 348.09 0.96283 3 ; parmbsc0 ----> Will Stebbeds<br>CT CT CI OH 4 190.98 1.17804 -1 ; parmbsc0 ----> Will Stebbeds<br>CT CT CI OH 4 295.63 0.09210 -2 ; parmbsc0 ----> Will Stebbeds<br>CT CT CI OH 4 348.10 0.96283 3 ; parmbsc0 ----> Will Stebbeds<br><br>;i j k l func <br> X CI OS X 9 0.0 1.15000 3 ; parmbsc0 ----> Will Stebbeds<br> X CI OH X 9 0.0 0.50000 3 ; parmbsc0 ----> Will Stebbeds <br> X CI CT X 9 0.0 1.40000 3 ; PARMBSC0 ---> Will Stebbeds <br><br>As you can see func=1 was changed to func=4 and func=3 was changed to func=9.<br><br>This was the only way I could find in which the parameters would work, is it valid to make such alterations arbitrarily? The only other way it will work is if I comment out the repeated lines for the same 4 atoms.<br><br>Any help on this matter would be very much appreciated.<br><br>best regards<br><br>Will<br><br><br><br><br>> Date: Sat, 5 Feb 2011 12:23:32 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Porting Amber parmbsc0 force field to Gromacs<br>> <br>> <br>> <br>> william Stebbeds wrote:<br>> > Hello,<br>> > <br>> > I would like to use the parmbs0 Amber forcefield to Gromacs, <br>> > specifically the nucleic acid parameters.<br>> > <br>> > Is this likely to come in a future release?<br>> > <br>> <br>> Force fields are only implemented if a developer has a compelling reason to do <br>> so, and then take the time to validate it. As such, new force fields are not <br>> often introduced.<br>> <br>> > I appreciate that this will likely be a difficult process but if anyone <br>> > can point me in the right direction I would be very grateful.<br>> > <br>> <br>> You can probably take an existing Amber force field and modify it. Chapter 5 is <br>> your friend here. By modifying existing files, you don't have to come up with <br>> all the syntax by yourself.<br>> <br>> -Justin<br>> <br>> > Will - Cranfield University<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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