<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Dear Prof. David<DIV>Thanks for the suggestion. I just had a look for the various force field options. before starting my simulation I have a little queries..</DIV><DIV>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?</DIV><DIV>2)Can I use ffoplsaa (all atom force field) for the vacuum simulation? or should I use ffencadv for the simulation?</DIV><DIV>3) What does scaled-down vacuum charges mean? Is it different from the normal vacuum force field?</DIV><DIV>Many thanks and regards</DIV><DIV>Nav<BR><DIV><DIV> On Aug 17, 2006, at 9:11 AM, David van der Spoel wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Navratna Vajpai wrote:</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear Mark</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hello.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.<SPAN class="Apple-converted-space"> </SPAN></DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">use an all atom force field.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Best regards</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Nav</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Aug 17, 2006, at 5:46 AM, Mark Abraham wrote:</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Navratna Vajpai wrote:</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks and regards</DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Does your force field include explicit non-polar hydrogen atoms? Or does it use united atoms?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Mark</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN>gmx-users@gromacs.org <<A href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</A>></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org <<A href="mailto:gmx-users-request@gromacs.org">mailto:gmx-users-request@gromacs.org</A>>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">*******************************************</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Navratna Vajpai</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Ph. D student in Prof. Grzesiek's laboratory</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Structural Biology</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Biozentrum, University of Basel</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Klingelbergstrasse 70,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">CH-4056</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Basel, Switzerland.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Phone- +41 61 267 2080(O)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>+41 78 744 0810(M)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">navratna.vajpai@unibas.ch <<A href="mailto:navratna.vajpai@unibas.ch">mailto:navratna.vajpai@unibas.ch</A>></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">David.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">________________________________________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Husargatan 3, Box 596,<SPAN class="Apple-converted-space"> <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phone:<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>46 18 471 4205<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>fax: 46 18 511 755</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>spoel@gromacs.org <SPAN class="Apple-converted-space"> </SPAN>http://folding.bmc.uu.se</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. 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Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Kai; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Kai; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">*******************************************</SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Navratna Vajpai</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Ph. D student in Prof. Grzesiek's laboratory</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Department of Structural Biology</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Biozentrum, University of Basel</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Klingelbergstrasse 70,</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">CH-4056</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Basel, Switzerland.</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; ">Phone- +41 61 267 2080(O)</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-tab-span" style="white-space:pre; font-family: Helvetica; "><SPAN class="Apple-style-span" style="white-space: pre; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="white-space: pre; ; font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; white-space: pre; "><SPAN class="Apple-style-span" style="font-family: Helvetica; white-space: pre; "> </SPAN></SPAN></SPAN></SPAN></SPAN><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "> +41 78 744 0810(M)</SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><DIV style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><SPAN class="Apple-style-span" style="font-family: Helvetica; "><A href="mailto:navratna.vajpai@unibas.ch">navratna.vajpai@unibas.ch</A></SPAN></SPAN></DIV><DIV style="font-family: Helvetica; "><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></DIV></BODY></HTML>