Hi, I mistyped the command as you mentioned. I did used the following:
grompp -f eminimization.mdp -c insu_pwi2MM.pdb -p insu_pwi.top -o MM_insu.tpr Now the error is the following: 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: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (insu_pwi2MM.pdb, 21149) does not match topology (insu_pwi.top, 21157) Ram. On Mon, Jun 30, 2008 at 12:45 PM, Nuno Azoia <[EMAIL PROTECTED]> wrote: > Hi! > > I'm new to Gromacs, so maybe my answer is not 100% correct, but it seems to > me that you forgot to create the required insu_pwi2MM.gro file. In your last > pdb2gmx command you just created insu_pwi2MM.pdb, and then the last grompp > command cannot found the insu_pwi2MM.gro file. I think you have to repeat > the last pdb2gmx command in order to create the .gro file, something like > > pdb2gmx -f insu_pwi.pdb -p insu_pwi.top -o insu_pwi2MM.*gro* -inter –merge > -ignh > > (the same command you have written but with different output file) > > Nuno Azoia > > rams rams wrote: > >> 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]<mailto: >> [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]> >> <mailto:[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 >> <mailto: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] >> <mailto:[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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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] >> <mailto:[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 >> > > > -- > > Nuno Gonçalo Azoia Lopes > > Laboratório de Investigação em Acabamento > Departamento de Engenharia Têxtil > Universidade do Minho > Campus de Azurém > 4800-058 Guimarães > Portugal > > Tel: +351 253 510 280 - Ext: 517 289 > Fax: +351 253 510 293 > > Mobile: +351 965 382 487 > E-mail: [EMAIL PROTECTED] > > > _______________________________________________ > 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 >
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