Hi Gromacs users After many try this weekend with my problem with do_dssp I come back to the mailing list
First, as David said me last friday in a previous message I have test my dssp program with example of pdb file from the Protein Data Bank (1HRC) (with one protein configuration in it) It works ! the calculation of the secondary structure is made and i obtain an output. When i use this pdb with do_dssp with the following command /applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f test_template.pdb -o ss.xpm I obtain the menu and I choose 5 (MainChain) I obtained the follwing message: There are 103 residues in your selected group Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1# And the calculation is not made (I wait more than ten minutes) and i obtain no ss.xpm I dont understand what is the problem Thank you again for your help Stefane > Thanks Justin for your reply > > So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to test. > I obtained always the same error. > > Opening library file /applications/gromacs-3.2.1/share/top/ss.map > Reading frame 0 time -1.000 > Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# What error? It appears that do_dssp is backing up an old intermediate file that gets generated as part of the calculation. -Justin > > Note that the pdb seems correct because the secondary structure can be > obtained with Stride available in VMD. And my trajectory was made CHARMM > ffield. is this a problem in this case > > Thank a lot > > My story with do_dssp > > As suggested David and others i rename my pdb file with the extension .pdb > > i used the following command > > ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb > > A menu appears, I choose the group 1 (protein) and i obtained the error > message > > Opening library file /applications/gromacs-3.2.1/share/top/ss.map > Reading frame 0 time -1.000 > Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# > > What iis the problem. I give below a part of my pdb file > > ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00 > ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 > ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 > ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 > ATOM 5 C ACE 1 7.470 -8.140 -10.510 0.51 0.00 > ATOM 6 O ACE 1 7.594 -9.280 -10.074 -0.51 0.00 > ATOM 7 N GLY 2 8.125 -7.096 -10.030 -0.47 0.00 > ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 > ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 > ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 > ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 > ATOM 12 C GLY 2 10.408 -6.734 -9.033 0.51 0.00 > ATOM 13 O GLY 2 11.313 -7.365 -8.492 -0.51 0.00 > ATOM 14 N ASP 3 10.647 -5.532 -9.599 -0.47 0.00 > ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 > ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 > ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 > ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 > ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 > ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 > ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 > ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 > ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 > > Thank you again for your kindly help > > Stefane > > ABEL Stephane 175950 wrote: > > I used the following command > > > > ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a > part is show below. I obtained a segmentation fault. > > > > Maybe it is not a the good command. Remember that my trajectories are not > made/compatible with GROMACS and i have only a pdb coordinates of my MD. > > > don't rename the .pdb file to .tpr. Just use .pdb > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Jan 2008 09:30:47 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: Targeted MD > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Steven Kirk wrote: > > Mark Abraham <[EMAIL PROTECTED]> wrote > > >> "Non-Protein" serves well here. So a usual tc-grps line has "Protein > >> Non-Protein" for a protein simulation. > >> > >> Mark > > > > A supplementary question. > > > > The tc-grps line can take predefined standard group names such as > > 'System', 'Protein' and 'Non-Protein'. > > > > Does the 'Protein' group need to actually BE a protein, or are 'Protein' > > and 'Non-Protein' really synonyms for > > 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? > > I haven't read the code or found any mention in the manual, but I expect > that src/share/top/aminoacids.dat contains the names of any amino acids, > and thus implicitly defines these groups. > > Mark > > > ------------------------------ > > Message: 3 > Date: Fri, 11 Jan 2008 09:24:40 +0800 > From: "xuji"<[EMAIL PROTECTED]> > Subject: [gmx-users] Asking help about PME > To: "[email protected]" <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="gb2312" > > Hi all gromacs users: > > I am digging into the PME method in gromacs. Can someone tell > me what files have something to do with PME and the corresponding > method FFT? > > Thanks! > ¡¡¡¡ > > > Best wishes! > > Ji Xu > Institute of Process Engineering > Chinese Academy of Sciences > P.O.Box 353, Beijing, 100080, China > Tel: +86-10-82627076 > Fax:+86-10-62558065 > [EMAIL PROTECTED] > > 2008-01-11 > ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/ca6a4e79/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Fri, 11 Jan 2008 13:10:11 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Asking help about PME > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=GB2312 > > xuji wrote: > > > > Hi all gromacs users: > > > > I am digging into the PME method in gromacs. Can someone tell > > me what files have something to do with PME and the corresponding > > method FFT? > > >From the gromacs source directory, try > > find * -name "*pme*" > > and > > grep -i pme src/*/*.c include/*.h include/*/*.h | grep -v -i development > > Mark > > > ------------------------------ > > Message: 5 > Date: Fri, 11 Jan 2008 10:44:05 +0800 > From: Yang Ye <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Asking help about PME > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/295b0c2d/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Fri, 11 Jan 2008 09:55:19 +0530 (IST) > From: [EMAIL PROTECTED] > Subject: [gmx-users] (no subject) > To: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > Hi all, > I have been trying to generate .rtp, .top files from having input of .gro > file for particular molecule in gromacs. I tried this with (x2top) command > implemented in gromacs but i have encountered a problem while executing > this command , that i am mentioning below. > > Fatal error: Library file ffG43a1.n2t not found in current dir nor in > default directories. > (You can set the directories to search with the GMXLIB path variable.) > > So how do i will be able to resolve this problem. > If i will be getting any help i will be very thankful for you. > > Kinshuk Raj Srivastava > IIT-Bombay > India > > > > > ------------------------------ > > Message: 7 > Date: Fri, 11 Jan 2008 10:02:06 +0530 (IST) > From: [EMAIL PROTECTED] > Subject: [gmx-users] x2top & Library file ffG43a1.n2t > To: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > > Hi all, > I have been trying to generate .rtp, .top files from having input of .gro > file for particular molecule in gromacs. I tried this with (x2top) command > implemented in gromacs but i have encountered a problem while executing > this command , that i am mentioning below. > > Fatal error: Library file ffG43a1.n2t not found in current dir nor in > default directories. > (You can set the directories to search with the GMXLIB path variable.) > > So how do i will be able to resolve this problem. > If i will be getting any help i will be very thankful for you. > > Kinshuk Raj Srivastava > IIT-Bombay > India > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > > > > > ------------------------------ > > Message: 8 > Date: Fri, 11 Jan 2008 16:23:52 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] (no subject) > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > [EMAIL PROTECTED] wrote: > > Hi all, > > I have been trying to generate .rtp, .top files from having input of .gro > > file for particular molecule in gromacs. I tried this with (x2top) command > > implemented in gromacs but i have encountered a problem while executing > > this command , that i am mentioning below. > > > > Fatal error: Library file ffG43a1.n2t not found in current dir nor in > > default directories. > > (You can set the directories to search with the GMXLIB path variable.) > > > > So how do i will be able to resolve this problem. > > If i will be getting any help i will be very thankful for you. > > So what value does GMXLIB have? What value should it have? Where did you > install GROMACS? Can you find this file anywhere? Have you read the > x2top documentation? > > Mark > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 45, Issue 32 > ***************************************** > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/ms-tnef > Size: 6833 bytes > Desc: not available > Url : > http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/94d28610/attachment.bin > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 45, Issue 36 > ***************************************** > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== ------------------------------ Message: 2 Date: Fri, 11 Jan 2008 11:01:58 -0500 From: "Justin A. Lemkul" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] chromophore parameters for Molecular Dynamics To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Quoting Anthony Cruz <[EMAIL PROTECTED]>: > Hi users: > I am working in a new projec and we plan to do some molecular dynamic > experiment to an engineered GFP molecule. I have been searching for the > parameters for the GFP chromophore without success. Can some one help me? Any > reference or parameters?? Unless someone has already developed them, you'll have to do it yourself (not an easy task). See here: http://wiki.gromacs.org/index.php/Exotic_Species and http://wiki.gromacs.org/index.php/Parameterization -Justin > > Best Regards, > Anthony > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== ------------------------------ Message: 3 Date: Fri, 11 Jan 2008 12:34:51 -0500 From: "Myunggi Yi" <[EMAIL PROTECTED]> Subject: [gmx-users] Re: Invalid order for directive defaults To: "Discussion list for GROMACS users" <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" I solved the problem. I found one more "ffgmx.itp" in my pro.itp. On Jan 11, 2008 12:29 PM, Myunggi Yi <[EMAIL PROTECTED]> wrote: > Dear gromca users, > > I'm a new user of gromacs. > I'm trying to run energy minimization on the system of a short peptide and > a lipid bilayer. > The following is my top file. > > ++++++++++++++++++++ > ; > #include "ffgmx.itp" > #include "../lipid.popc.itp" > #include "popc.itp" > #include "pro.itp" > #include "ions.itp" > #include "spc.itp" > > > [ system ] > ; name > Fusion peptide on POPC > > [ molecules ] > ; name number > Protein 1 > POPC 128 > Na 2 > SOL 3655 > +++++++++++++++++++ > > > > And I copied em.mdp with a little modification from the tutorial. > > > > +++++++++++++++++++ > ; User spoel (236) > ; Wed Nov 3 17:12:44 1993 > ; Input file > ; > cpp = cpp > define = -DPOSRES > constraints = none > integrator = steep > nsteps = 100 > ; > ; Energy minimizing stuff > ; > emtol = 2000 > emstep = 0.01 > > nstcomm = 1 > ns_type = grid > rlist = 1 > rcoulomb = 1.0 > rvdw = 1.0 > Tcoupl = no > Pcoupl = no > gen_vel = no > ++++++++++++++++++ > > > After runing grompp I've got the following error message. > > > ++++++++++++++++++++++ > Program grompp, VERSION 3.3.1 > Source code file: topio.c, line: 388 > > Fatal error: > Invalid order for directive defaults, file > ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", > line 4 > ++++++++++++++++++++ > > I think I have only one [ defaults ] section. > Does Anybody have an idea? What is wrong? > > Have a great day. > > > -- > Best wishes, > > MYUNGGI YI > ================================== > KLB 419 > Institute of Molecular Biophysics > Florida State University > Tallahassee, FL 32306 > > Office: (850) 645-1334 > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> -- Best wishes, MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/99bda33a/attachment-0001.html ------------------------------ Message: 4 Date: Fri, 11 Jan 2008 12:29:59 -0500 From: "Myunggi Yi" <[EMAIL PROTECTED]> Subject: [gmx-users] Invalid order for directive defaults To: "Discussion list for GROMACS users" <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Dear gromca users, I'm a new user of gromacs. I'm trying to run energy minimization on the system of a short peptide and a lipid bilayer. The following is my top file. ++++++++++++++++++++ ; #include "ffgmx.itp" #include "../lipid.popc.itp" #include "popc.itp" #include "pro.itp" #include "ions.itp" #include "spc.itp" [ system ] ; name Fusion peptide on POPC [ molecules ] ; name number Protein 1 POPC 128 Na 2 SOL 3655 +++++++++++++++++++ And I copied em.mdp with a little modification from the tutorial. +++++++++++++++++++ ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = cpp define = -DPOSRES constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no ++++++++++++++++++ After runing grompp I've got the following error message. ++++++++++++++++++++++ Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive defaults, file ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"", line 4 ++++++++++++++++++++ I think I have only one [ defaults ] section. Does Anybody have an idea? What is wrong? Have a great day. -- Best wishes, MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080111/0e299745/attachment.html ------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 45, Issue 38 *****************************************
<<winmail.dat>>
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
