Re: [gmx-users] Hi ..

[Navratna Vajpai]

Dear Prof. David Thanks for the suggestion. I just had a look for the various force field options. before starting my simulation I have a little queries.. 1) Can I not use the same GROMOS force field g43b1 and then add HA afterwards by any other software or any other program in your package? 2)Can I use ffoplsaa (all atom force field) for the vacuum simulation? or should I use ffencadv for the simulation? 3) What does scaled-down vacuum charges mean? Is it different from the normal vacuum force field? Many thanks and regards Nav  On Aug 17, 2006, at 9:11 AM, David van der Spoel wrote: Navratna Vajpai wrote: Dear Mark Hello. The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp file and fond that the HC is defined there which corresponds to Hydrogen attached to the Carbon. But somehow in the pdb outcome this is not there. the output pdb file contains only H atoms corresponding to HN. Now I exactly don't know which type of atoms are defined there. Kindly let me know what should I do to bring HA into the scene.  use an all atom force field. Best regards Nav On Aug 17, 2006, at 5:46 AM, Mark Abraham wrote: Navratna Vajpai wrote: Dear All I have been able to carry on with the MD run of my peptides. But when I converted the traj into the pdb file I realized that there are no HA atoms in the pdb. I checked the rtp file and found that even those atoms are not defined there. So can anyone tell me how to get the HA (after or before the MD run) as i need them explicitly . I was trying to look for the options available in the trjconv but could not find. Thanks and regards Does your force field include explicit non-polar hydrogen atoms? Or does it use united atoms? Mark _______________________________________________ gmx-users mailing list    gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O)        +41 78 744 0810(M) [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> ------------------------------------------------------------------------ _______________________________________________ gmx-users mailing list    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, Assoc. Prof., Molecular Biophysics group, 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 list    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 ******************************************* Navratna Vajpai Ph. D student in Prof. Grzesiek's laboratory Department of Structural Biology Biozentrum, University of Basel Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Phone- +41 61 267 2080(O)        +41 78 744 0810(M) [EMAIL PROTECTED]

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