Thanks Mark for your valuable reply and suggestions. If once i use "grompp" command its not showing any specific atom, its showing generally atomtype NR , HC, CR1 not found. <br>if we come to topic of forcefields, For lipids i didnt use any Force field due to popc.top and popc.itp files downloaded from Peter tielman<br>
website and incase of my protein i have used "GROMOS96 43a1 force field". <br>Pls help me.....<br>Thanks in advance.....<br><br><div class="gmail_quote">On Feb 19, 2008 12:51 PM, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Lennard Jones spheres (Mark Abraham)<br> 2. Re: Proline on OPLSSaa (Mark Abraham)<br>
3. Re: problem regarding .top file generated by genbox (Mark Abraham)<br> 4. RE:problem regarding .top file generated by genbox (sudheer babu)<br> 5. Re: RE:problem regarding .top file generated by genbox<br> (Mark Abraham)<br>
<br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Tue, 19 Feb 2008 11:12:04 +1100<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Lennard Jones spheres<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:47BA1ED4.7050201@anu.edu.au">47BA1ED4.7050201@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Chiara Parravicini wrote:<br>> Hi gromacs users,<br>><br>> I would like to add LJ spheres into the protein cavitities, but I don't<br>> know how to define input parameters and files to set the run. Should I<br>
> define spheres as "dummy atoms"? Any suggestion will be greatly appreciated!<br><br>How do you want these spheres to interact with the system?<br><br>Mark<br><br><br>------------------------------<br><br>Message: 2<br>
Date: Tue, 19 Feb 2008 11:13:41 +1100<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] Proline on OPLSSaa<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:47BA1F35.1020001@anu.edu.au">47BA1F35.1020001@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Mauro Puppett wrote:<br>> -----------------------------<br>
><br>> Sorry but I'm not able to solve the problem.<br>> I've added the impropers for ACE and PRO but I still have warnings.<br>> Checking the lines, the warning refers to the dihedrals of the methoxy group. I'm not able to find anywhere how to fix this problem.<br>
> Could you please help me again?<br><br>Probably, your force field doesn't have dihedrals for methoxy. You'll<br>have to parametrize yourself, or search the literature for others who<br>might have done it. Check out<br>
<a href="http://wiki.gromacs.org/index.php/Parameterization" target="_blank">http://wiki.gromacs.org/index.php/Parameterization</a><br><br>Mark<br><br><br>------------------------------<br><br>Message: 3<br>Date: Tue, 19 Feb 2008 11:15:42 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] problem regarding .top file generated by<br> genbox<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:47BA1FAE.2040904@anu.edu.au">47BA1FAE.2040904@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Justin A. Lemkul wrote:<br>> I suspect you have an error with the order that you have included the relevant<br>
> .itp files within your topology. It would be helpful to include a snapshot of<br>> your topology which illustrated the order in which these files are included.<br>><br>> Also, if you are asking whether your commands are right or not, you should<br>
> include your actual commands, otherwise our default assumption is "probably<br>> not." :-)<br><br>Yep, and also the OP didn't say what force field they were using. Since<br>this defines the atom types, and their problem was with unknown atom<br>
types, this information is important.<br><br>Mark<br><br><br>------------------------------<br><br>Message: 4<br>Date: Tue, 19 Feb 2008 11:53:14 +0530<br>From: "sudheer babu" <<a href="mailto:sudheer.pbm07@gmail.com">sudheer.pbm07@gmail.com</a>><br>
Subject: [gmx-users] RE:problem regarding .top file generated by<br> genbox<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a href="mailto:76de29310802182223o37bde3abi639d6e01b365671f@mail.gmail.com">76de29310802182223o37bde3abi639d6e01b365671f@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>Thanks for your reply Mr.justin<br>i am sending the commands and .itp file sequence<br>the command i have used for protein insertion into membrane is<br>genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro , this<br>
command was fine it ran without error.<br>Later<br>grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p<br>topol.top(generated by genbox) -o<br>em.tpr<br>when i ran this grompp command its showing that atom typr NR, HC, CR1 not<br>
found<br> i am pasting part of my topology file<br><br> This is your topology file<br>; "Move Over Hogey Bear" (Urban Dance Squad)<br>;<br>; Include forcefield parameters<br>#include "ffgmx.itp"<br>
#include "lipid.itp"<br>#include "popc.itp<br><br><br>17 N 3 HISH N 7 -0.28 14.0067 ; qtot<br>0.72<br> 18 H 3 HISH H 7 0.28 1.008 ; qtot<br>
1<br> 19 CH1 3 HISH CA 8 0 13.019 ; qtot<br>1<br> 20 CH2 3 HISH CB 8 0 14.027 ; qtot<br>1<br> 21 C 3 HISH CG 9 -0.05 12.011 ; qtot<br>
0.95<br> 22 NR 3 HISH ND1 9 0.38 14.0067 ; qtot<br>1.33<br> 23 H 3 HISH HD1 9 0.3 1.008 ; qtot<br>1.63<br> 24 CR1 3 HISH CD2 9 0 13.019 ; qtot<br>
1.63<br> 25 CR1 3 HISH CE1 9 -0.24 13.019 ; qtot<br>1.39<br> 26 NR 3 HISH NE2 9 0.31 14.0067 ; qtot<br>1.7<br> 27 H 3 HISH HE2 9 0.3 1.008 ; qtot<br>
2<br> 28 C 3 HISH C 10 0.38 12.011 ; qtot<br>2.38<br> 29 O 3 HISH O 10 -0.38 15.9994 ; qtot<br>2<br> 30 N 4 HISH N 11 -0.28 14.0067 ; qtot<br>
1.72<br> 31 H 4 HISH H 11 0.28 1.008 ; qtot<br>2<br> 32 CH1 4 HISH CA 12 0 13.019 ; qtot<br>2<br> 33 CH2 4 HISH CB 12 0 14.027 ; qtot<br>
2<br> 34 C 4 HISH CG 13 -0.05 12.011 ; qtot<br>1.95<br> 35 NR 4 HISH ND1 13 0.38 14.0067 ; qtot<br>2.33<br> 36 H 4 HISH HD1 13 0.3 1.008 ; qtot<br>
2.63<br> 37 CR1 4 HISH CD2 13 0 13.019 ; qtot<br>2.63<br> 38 CR1 4 HISH CE1 13 -0.24 13.019 ; qtot<br>2.39<br> 39 NR 4 HISH NE2 13 0.31 14.0067 ; qtot<br>
2.7<br> 40 H 4 HISH HE2 13 0.3 1.008 ; qtot<br>3<br> 41 C 4 HISH C 14 0.38 12.011 ; qtot<br>3.38<br> 42 O 4 HISH O 14 -0.38 15.9994 ; qtot<br>
3<br><br>366 N 41 PHE N 160 -0.28 14.0067 ; qtot<br>2.72<br> 367 H 41 PHE H 160 0.28 1.008 ; qtot<br>3<br> 368 CH1 41 PHE CA 161 0 13.019 ; qtot<br>
3<br> 369 CH2 41 PHE CB 161 0 14.027 ; qtot<br>3<br> 370 C 41 PHE CG 161 0 12.011 ; qtot<br>3<br> 371 C 41 PHE CD1 162 -0.1 12.011 ; qtot<br>
2.9<br> 372 HC 41 PHE HD1 162 0.1 1.008 ; qtot<br>3<br> 373 C 41 PHE CD2 163 -0.1 12.011 ; qtot<br>2.9<br> 374 HC 41 PHE HD2 163 0.1 1.008 ; qtot<br>
3<br> 375 C 41 PHE CE1 164 -0.1 12.011 ; qtot<br>2.9<br> 376 HC 41 PHE HE1 164 0.1 1.008 ; qtot<br>3<br> 377 C 41 PHE CE2 165 -0.1 12.011 ; qtot<br>
2.9<br> 378 HC 41 PHE HE2 165 0.1 1.008 ; qtot<br>3<br> 379 C 41 PHE CZ 166 -0.1 12.011 ; qtot<br>2.9<br> 380 HC 41 PHE HZ 166 0.1 1.008 ; qtot<br>
3<br> 381 C 41 PHE C 167 0.38 12.011 ; qtot<br>3.38<br> 382 O 41 PHE O 167 -0.38 15.9994 ; qtot<br>3<br><br>; Include Position restraint file<br>#ifdef POSRES<br>
#include "posre.itp"<br>#endif<br><br>; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>protein in popc in water<br><br>[ molecules ]<br>; Compound #mols<br>
Protein 1<br>POPC 98<br>CL- 3<br>SOL 2457<br>Thanks in advance.<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20080219/b958713a/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20080219/b958713a/attachment-0001.html</a><br>
<br>------------------------------<br><br>Message: 5<br>Date: Tue, 19 Feb 2008 18:20:55 +1100<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] RE:problem regarding .top file generated by<br>
genbox<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:47BA8357.5000609@anu.edu.au">47BA8357.5000609@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>sudheer babu wrote:<br>> Thanks for your reply Mr.justin<br>> i am sending the commands and .itp file sequence<br>> the command i have used for protein insertion into membrane is<br>
> genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro ,<br>> this command was fine it ran without error.<br>> Later<br>> grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p topol.top<br>
> (generated by genbox) -o em.tpr<br>> when i ran this grompp command its showing that atom typr NR, HC, CR1<br>> not found<br>> i am pasting part of my topology file<br><br>This is very hard to read. English uses capitalization of names and<br>
first words in sentences, and punctuation, all to increase readability.<br>People are trained to read text where this occurs, and if you do not do<br>it then people find your work hard to read. They might well give up on<br>
reading it, and when you're looking for free help, that's the last thing<br>you want to do!<br><br>When moving in and out of English (into say, quoting GROMACS commands)<br>then you should indicate this with quotation marks "grompp -f em.mdp..."<br>
, or starting new paragraphs:<br><br> grompp -f em.mdp ...<br><br>Yes, this is more work for you, however not doing that work is a false<br>economy - you lose people who don't bother to read your post at all.<br><br>
> This is your topology file<br>> ; "Move Over Hogey Bear" (Urban Dance Squad)<br>> ;<br>> ; Include forcefield parameters<br>> #include "ffgmx.itp"<br><br>This force field is deprecated. That means you shouldn't be using it<br>
without a sound reason. It also doesn't define the atom types that<br>grompp is complaining about. I guess that you did pdb2gmx on your<br>protein with one of the ffGxxx forcefields and are now mixing force<br>fields. DON'T! See <a href="http://wiki.gromacs.org/index.php/Force_Fields" target="_blank">http://wiki.gromacs.org/index.php/Force_Fields</a> and<br>
links thereon.<br><br>> [ molecules ]<br>> ; Compound #mols<br>> Protein 1<br>> POPC 98<br>> CL- 3<br>> SOL 2457<br><br>Don't do this either... see <a href="http://wiki.gromacs.org/index.php/Thermostats" target="_blank">http://wiki.gromacs.org/index.php/Thermostats</a><br>
<br>Mark<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" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br><br>End of gmx-users Digest, Vol 46, Issue 56<br>*****************************************<br>
</blockquote></div><br>