Everything went fine at this point. Thanks David.<br>
<br>
My protein has 1343 atoms in it, but when I try to make an index file,
it is going from 1 - 1336, the only reason i can think is when I use
-inter option, I protonated 7 OE2 in GLU residue, so the difference of
1343 and 1336. But dont you think , the index file of protein should
run from 1-1343 and then the bilayer indices start.<br>
In my case, the index file of the bilayer is starting from 1337, while
in the pdb file, it is from 1344, should I manually change them?? I
hope yes.<br>
Thanks and Merrry X-mas to everyone,<br>
Vissu<br><br><div><span class="gmail_quote">On 12/22/05, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Viswanadham Sridhara wrote:<br>> Just a continuation of my previous email, I was wondering how the<br>> interactions between protein and lipid bilayer are included, should I<br>> put the option "yes" in generate pairs in
ffgmx.itp or how does it work?<br>> I know its a naive question though....<br>Not naive, but it is written in the manual. Anyway, the parameters are<br>already in ffgmx.itp<br><br>> Thanks,<br>><br>><br>> On 12/22/05, *Viswanadham Sridhara* <
<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a><br>> <mailto:<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a>>> wrote:<br>><br>> Hi David,<br>> I did with -inter option and it worked, now I got the itp file for
<br>> protein.<br>> And I have taken dppc bilayer from Dr.Tieleman's website, and I<br>> inserted protein in bilayer.<br>> Now my question is, should my topology file look like this:<br>> #include "
ffgmx.itp"<br>> #include "protein.itp"<br>> #include "dppc.itp".......and so on.<br>> I got an error while running energy minimisation,<br>> it ended saying fmax norm is infinity on one atom, should I do any
<br>> other steps in between, am using flexible water for EM.<br>> Thanks in advance,<br>> Vissu<br>><br>><br>> On 12/21/05, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Viswanadham Sridhara wrote:<br>><br>>> The only problem with my pdb file is that it has 1330 atoms, I
<br>> 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 -<br>> 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<br>> 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<br>> 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<br>> 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<br>> 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<br>> other way<br>>> pdb2gmx can take care of this.<br>><br>><br>> No, you should run pdb2gmx -inter and select GLUH for the
<br>> residue in<br>> question. This will put the proton on OE1, but that should still<br>> give<br>> the same effect.<br>><br>>> Thanks in advance,<br>>> Vissu
<br>>><br>>><br>>> On 12/21/05, *David van der Spoel* < <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>><br>>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>>><br>> 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<br>> between, is<br>>> there<br>>> > any way that I can add them at the end, but give the
<br>> respective<br>>> > residue number, or should they be in order and represent<br>> .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>>> >_______________________________________________<br>>> >gmx-users mailing list<br>>> ><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <mailto: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>>><br>>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> <<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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 href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>><br>>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>>.<br>>> ><br>>><br>>><br>>> --<br>>> David.<br>>><br>
> ________________________________________________________________________<br>><br>>> David van der Spoel, PhD, Assoc. Prof., Molecular<br>> 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 href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a><br>>
<mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>>
<a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><br>> <mailto:<a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a>><br>>> <mailto:<a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <mailto:<a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a>>><br>> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>>> <<a href="http://xray.bmc.uu.se/%7Espoel">
http://xray.bmc.uu.se/%7Espoel</a><br>> <<a href="http://xray.bmc.uu.se/%7Espoel">http://xray.bmc.uu.se/%7Espoel</a>>><br>>><br>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>><br>>><br>>> _______________________________________________<br>>> gmx-users mailing list<br>>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>><br>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>>>
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</a>><br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>><br>>> <mailto: <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:
<a href="mailto:gmx-users-request@gromacs.org">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>>>_______________________________________________
<br>>>gmx-users mailing list<br>>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">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 href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <mailto:<a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a>><br>> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>><br>><br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> <<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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<br>> Graduate Research Assistant,<br>> Old Dominion University, "VIRGINIA".<br>><br>><br>><br>><br>> --<br>> Viswanadham Sridhara,<br>> Graduate Research Assistant,<br>> Old Dominion University, "VIRGINIA".
<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">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 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<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 href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________
<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">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 href="mailto:gmx-users-request@gromacs.org">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>