Yes, Mark i have taken a look in your previous message To test my dssp program I took a pdb from the protein data bank: 1HRC. This pdb contains only one protein (and one frame). The DSSP program works fine with it and I obtain an output. So To test my do_dssp i also used this pdb. In this case when i choose MainChain 5 or other choices I obtain the same message described below and no output. I think, I have set correctly the DSSP environment variable because i have not the Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP). Moreover i think that ten minutes is not to short to process one config indeed the DSSP program take less than 2 seconds to compute the secondary structure of the protein in 1HRC pdb file.
So i very frustrated... Stefane ABEL Stephane 175950 wrote: > 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 This could easily be too short a time if there are multiple frames in your pdb file. I don't know whether you have or need to follow the suggestion I made last time... http://www.gromacs.org/pipermail/gmx-users/2008-January/031720.html Also, per "man do_dssp" you need to have set your DSSP environment variable correctly. Finally, test do_dssp on the same .pdb file you say works with dssp. Mark ------------------------------ Message: 2 Date: Mon, 14 Jan 2008 09:45:33 -0200 From: [EMAIL PROTECTED] Subject: [gmx-users] grompp problem with trr input option.... To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Hi all When I run grompp with a trr input file using the command line showed below grompp -np 2 -t run_1.trr -f md_2 -p topol_2.top -o run_2 it gives me a error: Program grompp, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: conf.gro Could anyone tell me how I can fix it? Thank you in advance. Sergio Garay Biochemist Facultad de Bioq. y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina ------------------------------ Message: 3 Date: Mon, 14 Jan 2008 12:59:31 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] grompp problem with trr input option.... 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 > > When I run grompp with a trr input file using the command line showed below > > grompp -np 2 -t run_1.trr -f md_2 -p topol_2.top -o run_2 > > it gives me a error: > > Program grompp, VERSION 3.3.1 > Source code file: futil.c, line: 340 > > File input/output error: > conf.gro > > Could anyone tell me how I can fix it? you need to supply a conf as well. it will not be used. > > Thank you in advance. > > Sergio Garay > Biochemist > Facultad de Bioq. y Cs. Biológicas > Universidad Nacional del Litoral > Santa Fe - Argentina > > > _______________________________________________ > 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 thewww > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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: 4 Date: Mon, 14 Jan 2008 08:44:04 -0800 (PST) From: Mufaddal Soni <[EMAIL PROTECTED]> Subject: [gmx-users] about details of the topology file. To: [email protected] Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Dear users, Thankyou for helping me regarding the topology file of my FNP inhibitor. I am facing one small problem understanding the topology file of my inhibitor. I have copied a part of my topology file. [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; OP1 F1 1 7 1 ; OP1 F2 1 8 1 ; OP1 C8 2 9 1 ; P1 C9 2 24 1 ; P1 C7 3 6 1 ; OP2 F1 3 7 1 ; OP2 F2 3 8 1 ; OP2 C8 4 6 1 ; OP3 F1 4 7 1 ; OP3 F2 4 8 1 ; OP3 C8 5 10 1 ; C1 C10 5 23 1 ; C1 C6 6 9 1 ; F1 C9 6 24 1 ; F1 C7 7 9 1 ; F2 C9 7 24 1 ; F2 C7 8 11 1 ; C8 C11 8 22 1 ; C8 C5 9 12 1 ; C9 C2 9 21 1 ; C9 C4 9 23 1 ; C9 C6 10 13 1 ; C10 C12 10 20 1 ; C10 C3 10 24 1 ; C10 C7 11 14 1 ; C11 F3 11 15 1 ; C11 F4 11 16 1 ; C11 P2 11 21 1 ; C11 C4 11 23 1 ; C11 C6 12 17 1 ; C2 OP5 12 18 1 ; C2 OP6 12 19 1 ; C2 OP4 12 22 1 ; C2 C5 13 21 1 ; C12 C4 14 17 1 ; F3 OP5 14 18 1 ; F3 OP6 14 19 1 ; F3 OP4 14 20 1 ; F3 C3 15 17 1 ; F4 OP5 15 18 1 ; F4 OP6 15 19 1 ; F4 OP4 15 20 1 ; F4 C3 16 20 1 ; P2 C3 20 23 1 ; C3 C6 21 24 1 ; C4 C7 what i dont get here is the significance of this pairing cos there are no bonds between these atoms. [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 1 120.0 585.8 120.0 585.8 ; OP1 P1 OP2 1 2 4 1 120.0 585.8 120.0 585.8 ; OP1 P1 OP3 1 2 5 1 109.6 397.5 109.6 397.5 ; OP1 P1 C1 3 2 4 1 120.0 585.8 120.0 585.8 ; OP2 P1 OP3 3 2 5 1 109.6 397.5 109.6 397.5 ; OP2 P1 C1 4 2 5 1 109.6 397.5 109.6 397.5 ; OP3 P1 C1 2 5 6 1 109.5 397.5 109.5 397.5 ; P1 C1 F1 2 5 7 1 109.5 397.5 109.5 397.5 ; P1 C1 F2 2 5 8 1 109.5 397.5 109.5 397.5 ; P1 C1 C8 6 5 7 1 109.5 397.5 109.5 397.5 ; F1 C1 F2 6 5 8 1 109.5 397.5 109.5 397.5 ; F1 C1 C8 7 5 8 1 109.5 397.5 109.5 397.5 ; F2 C1 C8 5 8 9 1 120.0 418.4 120.0 418.4 ; C1 C8 C9 5 8 24 1 120.0 418.4 120.0 418.4 ; C1 C8 C7 9 8 24 1 120.0 418.4 120.0 418.4 ; C9 C8 C7 8 9 10 1 120.0 418.4 120.0 418.4 ; C8 C9 C10 9 10 11 1 120.0 418.4 120.0 418.4 ; C9 C10 C11 9 10 22 1 120.0 418.4 120.0 418.4 ; C9 C10 C5 11 10 22 1 120.0 418.4 120.0 418.4 ; C11 C10 C5 10 11 12 1 120.0 418.4 120.0 418.4 ; C10 C11 C2 11 12 13 1 120.0 418.4 120.0 418.4 ; C11 C2 C12 11 12 20 1 120.0 418.4 120.0 418.4 ; C11 C2 C3 13 12 20 1 120.0 418.4 120.0 418.4 ; C12 C2 C3 12 13 14 1 109.5 397.5 109.5 397.5 ; C2 C12 F3 12 13 15 1 109.5 397.5 109.5 397.5 ; C2 C12 F4 12 13 16 1 109.5 397.5 109.5 397.5 ; C2 C12 P2 14 13 15 1 109.5 397.5 109.5 397.5 ; F3 C12 F4 14 13 16 1 109.5 397.5 109.5 397.5 ; F3 C12 P2 15 13 16 1 109.5 397.5 109.5 397.5 ; F4 C12 P2 13 16 17 1 109.6 397.5 109.6 397.5 ; C12 P2 OP5 13 16 18 1 109.6 397.5 109.6 397.5 ; C12 P2 OP6 13 16 19 1 109.6 397.5 109.6 397.5 ; C12 P2 OP4 17 16 18 1 120.0 585.8 120.0 585.8 ; OP5 P2 OP6 17 16 19 1 120.0 585.8 120.0 585.8 ; OP5 P2 OP4 18 16 19 1 120.0 585.8 120.0 585.8 ; OP6 P2 OP4 12 20 21 1 120.0 418.4 120.0 418.4 ; C2 C3 C4 20 21 22 1 120.0 418.4 120.0 418.4 ; C3 C4 C5 10 22 21 1 120.0 418.4 120.0 418.4 ; C10 C5 C4 10 22 23 1 120.0 418.4 120.0 418.4 ; C10 C5 C6 21 22 23 1 120.0 418.4 120.0 418.4 ; C4 C5 C6 22 23 24 1 120.0 418.4 120.0 418.4 ; C5 C6 C7 8 24 23 1 120.0 418.4 120.0 418.4 ; C8 C7 C6 25 3 2 1 109.6 397.5 109.6 397.5 26 4 2 1 109.6 397.5 109.6 397.5 27 19 16 1 109.6 397.5 109.6 397.5 27 18 16 1 109.6 397.5 109.6 397.5 in this the 5th and 7th column i understand are the actual angles, but what do the 6th and 8th columns signify?? [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 2 1 4 3 2 35.3 836.8 35.3 836.8 ; imp P1 OP1 OP3 OP2 5 2 6 7 2 35.3 836.8 35.3 836.8 ; imp C1 P1 F1 F2 8 5 24 9 2 0.0 1673.6 0.0 1673.6 ; imp C8 C1 C7 C9 10 22 11 9 2 0.0 1673.6 0.0 1673.6 ; imp C10 C5 C11 C9 12 20 13 11 2 0.0 1673.6 0.0 1673.6 ; imp C2 C3 C12 C11 13 12 14 15 2 35.3 836.8 35.3 836.8 ; imp C12 C2 F3 F4 16 13 17 18 2 35.3 836.8 35.3 836.8 ; imp P2 C12 OP5 OP6 22 10 23 21 2 0.0 1673.6 0.0 1673.6 ; imp C5 C10 C6 C4 8 9 10 22 2 0.0 1673.6 0.0 1673.6 ; imp C8 C9 C10 C5 9 10 22 23 2 0.0 1673.6 0.0 1673.6 ; imp C9 C10 C5 C6 10 22 23 24 2 0.0 1673.6 0.0 1673.6 ; imp C10 C5 C6 C7 22 23 24 8 2 0.0 1673.6 0.0 1673.6 ; imp C5 C6 C7 C8 23 24 8 9 2 0.0 1673.6 0.0 1673.6 ; imp C6 C7 C8 C9 24 8 9 10 2 0.0 1673.6 0.0 1673.6 ; imp C7 C8 C9 C10 10 11 12 20 2 0.0 1673.6 0.0 1673.6 ; imp C10 C11 C2 C3 11 12 20 21 2 0.0 1673.6 0.0 1673.6 ; imp C11 C2 C3 C4 12 20 21 22 2 0.0 1673.6 0.0 1673.6 ; imp C2 C3 C4 C5 20 21 22 10 2 0.0 1673.6 0.0 1673.6 ; imp C3 C4 C5 C10 21 22 10 11 2 0.0 1673.6 0.0 1673.6 ; imp C4 C5 C10 C11 22 10 11 12 2 0.0 1673.6 0.0 1673.6 ; imp C5 C10 C11 C2 1 2 5 8 1 0.0 1.0 3 0.0 1.0 3 ; dih OP1 P1 C1 C8 1 2 5 8 1 0.0 3.1 2 0.0 3.1 2 ; dih OP1 P1 C1 C8 2 5 8 24 1 0.0 1.0 3 0.0 1.0 3 ; dih P1 C1 C8 C7 2 5 8 24 1 0.0 3.1 2 0.0 3.1 2 ; dih P1 C1 C8 C7 11 12 13 16 1 0.0 1.0 3 0.0 1.0 3 ; dih C11 C2 C12 P2 11 12 13 16 1 0.0 3.1 2 0.0 3.1 2 ; dih C11 C2 C12 P2 12 13 16 19 1 0.0 1.0 3 0.0 1.0 3 ; dih C2 C12 P2 OP4 12 13 16 19 1 0.0 3.1 2 0.0 3.1 2 ; dih C2 C12 P2 OP4 Similarly here the 6th and 8th columns give the values of the dihedrals but i dont understand what the 7th and 9th column signify. Cheers, Mufaddal Soni. --------------------------------- Never miss a thing. Make Yahoo your homepage. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080114/796d714c/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 48 *****************************************
<<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
