<div>Just a continuation of my previous email, I was wondering how the interactions between protein and lipid bilayer are included, should I put the option "yes" in generate pairs in ffgmx.itp or how does it work? I know its a naive question though....
</div>
<div>Thanks,<br><br> </div>
<div><span class="gmail_quote">On 12/22/05, <b class="gmail_sendername">Viswanadham Sridhara</b> <<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>Hi David,</div>
<div>I did with -inter option and it worked, now I got the itp file for protein.</div>
<div>And I have taken dppc bilayer from Dr.Tieleman's website, and I inserted protein in bilayer.</div>
<div>Now my question is, should my topology file look like this:</div>
<div>#include "ffgmx.itp"</div>
<div>#include "protein.itp"</div>
<div>#include "dppc.itp".......and so on.</div>
<div>I got an error while running energy minimisation,</div>
<div>it ended saying fmax norm is infinity on one atom, should I do any other steps in between, am using flexible water for EM.</div>
<div>Thanks in advance,</div>
<div>Vissu<br><br> </div>
<div><span class="e" id="q_10853dfbdcaf6039_1">
<div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">David van der Spoel</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se
</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Viswanadham Sridhara wrote:<br><br>> The only problem with my pdb file is that it has 1330 atoms, I think I
<br>> cant use prodrg with more than 300.......<br>> As you pointed out, I will try to make a decent pdb file.<br>><br>> One more question,<br>> This is a part of my .itp file<br>><br>> 295 N 40 GLU N 206 -
0.28 14.0067 ;<br>> qtot -1.28<br>> 296 H 40 GLU H 206 0.28 1.008<br>> ; qtot -1<br>> 297 CH1 40 GLU CA 207 0 13.019<br>> ; qtot -1
<br>> 298 CH2 40 GLU CB 208 0 14.027<br>> ; qtot -1<br>> 299 CH2 40 GLU CG 209 0 14.027<br>> ; qtot -1<br>> 300 C 40 GLU CD 210
0.27 12.011<br>> ; qtot -0.73<br>> 301 OM 40 GLU OE1 210 -0.635 15.9994<br>> ; qtot -1.365<br>> 302 OM 40 GLU OE2 210 -0.635 15.9994<br>> ; qtot -2
<br>> 303 C 40 GLU C 211 0.38 12.011<br>> ; qtot -1.62<br>> 304 O 40 GLU O 211 -0.38 15.9994<br>> ; qtot -2<br>><br>> while in pdb file,
<br>><br>> ATOM 295 N GLU 40 20.250 25.090 41.950 1.00 0.00<br>> ATOM 296 H GLU 40 20.340 25.930 41.420 1.00 0.00<br>> ATOM 297 CA GLU 40 20.620 25.440 43.320
1.00 0.00<br>> ATOM 298 CB GLU 40 21.210 26.840 43.440 1.00 0.00<br>> ATOM 299 CG GLU 40 22.630 26.980 42.910 1.00 0.00<br>> ATOM 300 CD GLU 40 23.050 28.450 42.940
1.00 0.00<br>> ATOM 301 OE1 GLU 40 22.680 29.310 42.130 1.00 0.00<br>> ATOM 302 OE2 GLU 40 23.780 28.750 44.050 1.00 0.00<br>> ATOM 303 HE2 GLU 40 24.010 29.710 43.890
1.00 0.00<br>> ATOM 304 C GLU 40 19.560 25.240 44.400 1.00 0.00<br>> ATOM 305 O GLU 40 19.800 24.810 45.530 1.00 0.00<br>><br>> if you can see, HE2 is missing in .itp file, when i used pdb2gmx
<br>> program, this might be due to its description in ffgmx.rtp file which is<br>> [ GLU ]<br>> [ atoms ]<br>> N N -0.280 0<br>> H H 0.280 0<br>> CA CH1 0.000 1
<br>> CB CH2 0.000 2<br>> CG CH2 0.000 3<br>> CD C 0.270 4<br>> OE1 OM -0.635 4<br>> OE2 OM -0.635 4<br>> C C 0.380 5<br>> O O -
0.380 5<br>><br>> %%%%%%%%%%%<br>> Should I add that atom type in .rtp file, or is there any other way<br>> pdb2gmx can take care of this.<br><br><br>No, you should run pdb2gmx -inter and select GLUH for the residue in
<br>question. This will put the proton on OE1, but that should still give<br>the same effect.<br><br>> Thanks in advance,<br>> Vissu<br>><br>><br>> On 12/21/05, *David van der Spoel* <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se" target="_blank">
spoel@xray.bmc.uu.se</a><br>> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Viswanadham Sridhara wrote:
<br>><br>> ><br>> > Hi Everyone, <br>> > I have a .itp file, where I want to add new atoms in between, is<br>> there<br>> > any way that I can add them at the end, but give the respective
<br>> > residue number, or should they be in order and represent .pdb file. <br>><br>><br>> Not easy (ch. 5). Try other means, maybe prodrg, or make a good<br>> pdb file<br>> from it (if it is a protein).
<br>><br>> > Thanks,<br>> > -Vissu<br>> > -- <br>> ><br>> >------------------------------------------------------------------------<br>><br>> ><br>> >_______________________________________________
<br>> >gmx-users mailing list <br>> ><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">
gmx-users@gromacs.org</a>><br>> > <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>> >Please don't post (un)subscribe requests to the list. Use the<br>> >www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">
gmx-users-request@gromacs.org</a><br>> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>> >
<br>><br>><br>> --<br>> David.<br>> ________________________________________________________________________ <br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala University.
<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755 <br>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se" target="_blank">
spoel@xray.bmc.uu.se</a><br>> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@gromacs.org" target="_blank">
spoel@gromacs.org </a><br>> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://xray.bmc.uu.se/~spoel" target="_blank">
http://xray.bmc.uu.se/~spoel</a><br>> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://xray.bmc.uu.se/%7Espoel" target="_blank">http://xray.bmc.uu.se/%7Espoel </a>><br>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>><br>> _______________________________________________<br>> gmx-users mailing list<br>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">
gmx-users@gromacs.org</a> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users </a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">
gmx-users-request@gromacs.org</a><br>> <mailto: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>>
<br>><br>><br>><br>> --<br>> Viswanadham Sridhara,<br>> Graduate Research Assistant,<br>> Old Dominion University, "VIRGINIA". <br>><br>>------------------------------------------------------------------------
<br>><br>>_______________________________________________<br>>gmx-users mailing list<br>><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank"> gmx-users@gromacs.org
</a><br>><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>Please don't post (un)subscribe requests to the list. Use the
<br>>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>><br><br><br>--<br>David.<br>
________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, <br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden
<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se </a> <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@gromacs.org" target="_blank">
spoel@gromacs.org</a> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://xray.bmc.uu.se/~spoel" target="_blank">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br><br>_______________________________________________<br>gmx-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users </a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all">
<br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".<br></span></div></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,
<br>Old Dominion University, "VIRGINIA".<br>