is that fine if i change the SOL number in the top file created at the first step ?
On Mon, Jun 30, 2008 at 1:50 PM, rams rams <[EMAIL PROTECTED]> wrote: > Here's where your problem is. This step is unnecessary! Once you have the > topology, there is no need to re-process with pdb2gmx. Once you have added > solvent and ions, simply make the changes to your topology with a text > editor. > > Could you explain what changes I should make in the topology file ?? > > > > > On Mon, Jun 30, 2008 at 1:44 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > >> >> >> 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) >>> >> >> Well, assuming you have all the correct hydrogens in the right place, >> that's fine, but in general, it is very easy to let pdb2gmx do the work for >> you and use -ignh. If it generated the topology for you, then that's fine. >> >> 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 >>> >>> >> Here's where your problem is. This step is unnecessary! Once you have >> the topology, there is no need to re-process with pdb2gmx. Once you have >> added solvent and ions, simply make the changes to your topology with a text >> editor. >> >> grompp -f eminimization.mdp -c insu_pwi2MM.gro -p insu_pwi.top -o >>> MM_insu.tpr >>> >>> >>> >> It has already been correctly pointed out by another user that you >> specified -o .pdb in the above step, but then called for the .gro equivalent >> here. That would be a problem. >> >> Basically, once the genion step is done, and you have made the appropriate >> changes to the topology (which can also be done with the -p flag of genion), >> then proceed to grompp. >> >> This makes much more sense, and it is easier to get help when it is >> clearly presented like this! >> >> -Justin >> >> >>> 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 [email protected] >>> <mailto:[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] >>> <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 [email protected] >>> <mailto:[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] >>> <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 | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >
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