Dear Justin, I am absolutely sorry for the discomfort. Since this is the first time I am using Gromacs, so things are not clear to me so I am trying things very randomly thats why I could not keep update the things. Here I restarted every thing and have a look at and let me know your suggestions:
pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb –ter –merge (since I removed all the hydrogens in my starting insu.pdb so didnt used -ignh here) editconf -f insu_p.pdb -o insu_pb.pdb -box 6.0 6.0 6.0 -center 3.0 3.0 3.0 genbox -cp insu_pb.pdb -cs spc216.gro -o insu_pw.pdb -p insu_p.top grompp -f eminimization.mdp -c insu_pw.pdb -p insu_p.top -o MM_insu.tp genion -s MM_insu.tpr -o insu_pwi.pdb -conc 0.008 –neutral pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.pdb -inter –merge -ignh grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o MM_insu.tpr The following is the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 716 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1046 of the 2628 1-4 parameter combinations Excluding 3 bonded neighbours for Protein 1 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 6878 turning all bonds into constraints... NOTE: System has non-zero total charge: -2.000000e+00 processing coordinates... ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: insu_pwi2MM.gro Ram. On Mon, Jun 30, 2008 at 6:45 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > It would be helpful if all of this was on one thread, with replies > embedded. I have sent several replies to your questions, all of which have > gone unacknowledged. It makes it very difficult for anyone (myself or > someone else) to give advice if we don't know what you're doing or what > you've tried. Even if something didn't work based on what I, or anyone > else, tells you, it is nice to know that "I tried this, but I still have a > problem, which is shown here: (exact error/warning/problem)." > > As I've said before, exact procedural details of what you've done are > essential for sorting out strange problems like this. This means - *exact* > (copy and paste) command lines from pdb2gmx, and any error messages you > receive. Also, any manipulations you have made to your input .pdb file. It > seems to me that you've probably edited your file to have only one chain > identifier, and hence why pdb2gmx is trying to make everything one molecule. > > The -merge option of pdb2gmx is what you want (see pdb2gmx -h). If the > following command line doesn't work, it would be nice to see an exact reason > (i.e., copy/paste from the error/warning/whatever): > > pdb2gmx -f (input).pdb -ignh -ter -merge > > I got the above to work perfectly on an insulin structure I found in the > RCSB (1ZNI), after deleting chains C and D from the .pdb file. If your > structure continues to give you headaches, try this one to make sure that > your Gromacs installation is working properly (something I inquired about > several days ago...) > > -Justin > > rams rams wrote: > >> HI, >> >> When I use the merge command along with pdb2gmx to form inter disulphide >> bonds between two different chains, its removing a water molecule to connect >> the two ends. Its like forming a peptide bond which I dont wish. Is there >> any way to tell to gromacs, to create the inter dishulphide bonds without >> creating the peptide bond between the two chains ? >> >> >> >> On Fri, Jun 27, 2008 at 6:51 PM, rams rams <[EMAIL PROTECTED] <mailto: >> [EMAIL PROTECTED]>> wrote: >> >> Hi, >> >> I have three di sulphide bonds in my crystal structure. In the >> topology file it left blanks at the corresponding sulphur >> connectivities (i.e., values corresponding to gb_, ga_. gd_ ). >> When I try to create the .tpr file it complains the following: >> >> processing topology... >> Generated 716 of the 2628 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 1 >> Generated 1046 of the 2628 1-4 parameter combinations >> WARNING 1 [file "insu_pwi.top", line 607]: >> No default G96Bond types, using zeroes >> WARNING 2 [file "insu_pwi.top", line 745]: >> No default G96Bond types, using zeroes >> WARNING 3 [file "insu_pwi.top", line 2008]: >> No default G96Angle types, using zeroes >> WARNING 4 [file "insu_pwi.top", line 2209]: >> No default G96Angle types, using zeroes >> WARNING 5 [file "insu_pwi.top", line 2345]: >> No default G96Angle types, using zeroes >> WARNING 6 [file "insu_pwi.top", line 2512]: >> No default G96Angle types, using zeroes >> WARNING 7 [file "insu_pwi.top", line 2748]: >> No default Proper Dih. types, using zeroes >> WARNING 8 [file "insu_pwi.top", line 2820]: >> No default Proper Dih. types, using zeroes >> WARNING 9 [file "insu_pwi.top", line 2863]: >> No default Proper Dih. types, using zeroes >> WARNING 10 [file "insu_pwi.top", line 2919]: >> No default Proper Dih. types, using zeroes >> Cleaning up temporary file gromppID2O6e >> ------------------------------------------------------- >> Program grompp, VERSION 3.3.1 >> Source code file: fatal.c, line: 416 >> >> Fatal error: >> Too many warnings, /usr/local2/gromacs/bin/grompp terminated >> ------------------------------------------------------- >> >> "Encountered Subspace Anomaly" (Star Trek) >> >> MD_insu.tpr was not created. Check for errors. Exiting ... >> >> Is there a way to fix it ? Also what are those b_, ga_. gd_ >> corresponds to ?? >> >> Ram. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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