Dear, Your tutorial for windows are lacking of proper guidence. You should post the steps to use it to make it more user friendly.
As I have tried from last two months but after installing it I really don't know to execute commands on windows. If you can guide me then why don't you not tell me the steps for using it on windows. On 11/10/09, gmx-users-requ...@gromacs.org <gmx-users-requ...@gromacs.org> wrote: > > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Missing H from residue (Jack Shultz) > 2. Re: Missing H from residue (Justin A. Lemkul) > 3. Re: Missing H from residue (Jack Shultz) > 4. Please tell me how to simulate two structures together in a > water box (radhika jaswal) > 5. (no subject) (pawan raghav) > 6. Re: (no subject) (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2009 21:38:23 -0500 > From: Jack Shultz <j...@drugdiscoveryathome.com> > Subject: Re: [gmx-users] Missing H from residue > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Cc: Andrey Voronkov <a...@drugdiscoveryathome.com> > Message-ID: > <6c65435e0911091838x89cddeera26061500376e...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > > > Jack Shultz wrote: > > > > <snip> > > > >> ------------------------------------------------------- > >> Program pdb2gmx, VERSION 4.0.5 > >> Source code file: pdb2gmx.c, line: 429 > >> > >> Fatal error: > >> Atom O in residue CARG 244 not found in rtp entry with 25 atoms > >> while sorting atoms > >> ------------------------------------------------------- > >> > >> But we got an O here > >> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 > >> O > >> > > > > The error is not telling you that the O atom is missing from the .pdb > file; > > it is telling you that it is present in the .pdb, but not in the .rtp > entry. > > Look at the .rtp entry for CARG > > [ CARG ] > [ atoms ] > N amber99_34 -0.34810 1 > H amber99_17 0.27640 2 > CA amber99_11 -0.30680 3 > HA amber99_19 0.14470 4 > CB amber99_11 -0.03740 5 > HB1 amber99_18 0.03710 6 > HB2 amber99_18 0.03710 7 > CG amber99_11 0.07440 8 > HG1 amber99_18 0.01850 9 > HG2 amber99_18 0.01850 10 > CD amber99_11 0.11140 11 > HD1 amber99_19 0.04680 12 > HD2 amber99_19 0.04680 13 > NE amber99_38 -0.55640 14 > HE amber99_17 0.34790 15 > CZ amber99_3 0.83680 16 > NH1 amber99_38 -0.87370 17 > HH11 amber99_17 0.44930 18 > HH12 amber99_17 0.44930 19 > NH2 amber99_38 -0.87370 20 > HH21 amber99_17 0.44930 21 > HH22 amber99_17 0.44930 22 > C amber99_2 0.85570 23 > OC1 amber99_45 -0.82660 24 > OC2 amber99_45 -0.82660 25 > > - you should have an O1 and O2 atom for the > > I made the following modification > ATOM 1900 O1 CARG 153 -17.391 > -20.267 11.508 1.00 0.00 O > ATOM 1909 O2 CARG 153 -18.666 > -19.390 13.107 1.00 0.00 O > > > ------------------------------------------------------- > Program pdb2gmx, VERSION 4.0.5 > Source code file: pdb2gmx.c, line: 429 > > Fatal error: > Atom O in residue CARG 122 not found in rtp entry with 25 atoms > while sorting atoms > ------------------------------------------------------- > > > > C-terminal carboxylate. > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > 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://lists.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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > > > ------------------------------ > > Message: 2 > Date: Mon, 09 Nov 2009 22:00:05 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Missing H from residue > To: "Gromacs Users' List" <gmx-users@gromacs.org> > Message-ID: <4af8d735.1030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Jack Shultz wrote: > > On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalem...@vt.edu> > wrote: > >> > >> Jack Shultz wrote: > >> > >> <snip> > >> > >>> ------------------------------------------------------- > >>> Program pdb2gmx, VERSION 4.0.5 > >>> Source code file: pdb2gmx.c, line: 429 > >>> > >>> Fatal error: > >>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms > >>> while sorting atoms > >>> ------------------------------------------------------- > >>> > >>> But we got an O here > >>> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 > >>> O > >>> > >> The error is not telling you that the O atom is missing from the .pdb > file; > >> it is telling you that it is present in the .pdb, but not in the .rtp > entry. > >> Look at the .rtp entry for CARG > > > > [ CARG ] > > [ atoms ] > > N amber99_34 -0.34810 1 > > H amber99_17 0.27640 2 > > CA amber99_11 -0.30680 3 > > HA amber99_19 0.14470 4 > > CB amber99_11 -0.03740 5 > > HB1 amber99_18 0.03710 6 > > HB2 amber99_18 0.03710 7 > > CG amber99_11 0.07440 8 > > HG1 amber99_18 0.01850 9 > > HG2 amber99_18 0.01850 10 > > CD amber99_11 0.11140 11 > > HD1 amber99_19 0.04680 12 > > HD2 amber99_19 0.04680 13 > > NE amber99_38 -0.55640 14 > > HE amber99_17 0.34790 15 > > CZ amber99_3 0.83680 16 > > NH1 amber99_38 -0.87370 17 > > HH11 amber99_17 0.44930 18 > > HH12 amber99_17 0.44930 19 > > NH2 amber99_38 -0.87370 20 > > HH21 amber99_17 0.44930 21 > > HH22 amber99_17 0.44930 22 > > C amber99_2 0.85570 23 > > OC1 amber99_45 -0.82660 24 > > OC2 amber99_45 -0.82660 25 > > > > - you should have an O1 and O2 atom for the > > > > I made the following modification > > ATOM 1900 O1 CARG 153 -17.391 > -20.267 11.508 1.00 0.00 O > > ATOM 1909 O2 CARG 153 -18.666 > -19.390 13.107 1.00 0.00 O > > > > Forgive my typo, what I meant was OC1 and OC2. You must always make sure > the > atoms in the structure file match those expected by the .rtp file. You > need OC1 > and OC2. > > -Justin > > > > > ------------------------------------------------------- > > Program pdb2gmx, VERSION 4.0.5 > > Source code file: pdb2gmx.c, line: 429 > > > > Fatal error: > > Atom O in residue CARG 122 not found in rtp entry with 25 atoms > > while sorting atoms > > ------------------------------------------------------- > > > > > >> C-terminal carboxylate. > >> > >> -Justin > >> > >> -- > >> ======================================== > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> 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://lists.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 gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > > > > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Mon, 9 Nov 2009 22:10:22 -0500 > From: Jack Shultz <j...@drugdiscoveryathome.com> > Subject: Re: [gmx-users] Missing H from residue > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: > <6c65435e0911091910r7c932c23l2a2814b72d8be...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks Justin! Got it now. > > On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > > > Jack Shultz wrote: > >> > >> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalem...@vt.edu> > wrote: > >>> > >>> Jack Shultz wrote: > >>> > >>> <snip> > >>> > >>>> ------------------------------------------------------- > >>>> Program pdb2gmx, VERSION 4.0.5 > >>>> Source code file: pdb2gmx.c, line: 429 > >>>> > >>>> Fatal error: > >>>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms > >>>> while sorting atoms > >>>> ------------------------------------------------------- > >>>> > >>>> But we got an O here > >>>> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00 > >>>> O > >>>> > >>> The error is not telling you that the O atom is missing from the .pdb > >>> file; > >>> it is telling you that it is present in the .pdb, but not in the .rtp > >>> entry. > >>> Look at the .rtp entry for CARG > >> > >> [ CARG ] > >> [ atoms ] > >> N amber99_34 -0.34810 1 > >> H amber99_17 0.27640 2 > >> CA amber99_11 -0.30680 3 > >> HA amber99_19 0.14470 4 > >> CB amber99_11 -0.03740 5 > >> HB1 amber99_18 0.03710 6 > >> HB2 amber99_18 0.03710 7 > >> CG amber99_11 0.07440 8 > >> HG1 amber99_18 0.01850 9 > >> HG2 amber99_18 0.01850 10 > >> CD amber99_11 0.11140 11 > >> HD1 amber99_19 0.04680 12 > >> HD2 amber99_19 0.04680 13 > >> NE amber99_38 -0.55640 14 > >> HE amber99_17 0.34790 15 > >> CZ amber99_3 0.83680 16 > >> NH1 amber99_38 -0.87370 17 > >> HH11 amber99_17 0.44930 18 > >> HH12 amber99_17 0.44930 19 > >> NH2 amber99_38 -0.87370 20 > >> HH21 amber99_17 0.44930 21 > >> HH22 amber99_17 0.44930 22 > >> C amber99_2 0.85570 23 > >> OC1 amber99_45 -0.82660 24 > >> OC2 amber99_45 -0.82660 25 > >> > >> - you should have an O1 and O2 atom for the > >> > >> I made the following modification > >> ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 > >> O > >> ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 > >> O > >> > > > > Forgive my typo, what I meant was OC1 and OC2. You must always make sure > > the atoms in the structure file match those expected by the .rtp > file. You > > need OC1 and OC2. > > > > -Justin > > > >> > >> ------------------------------------------------------- > >> Program pdb2gmx, VERSION 4.0.5 > >> Source code file: pdb2gmx.c, line: 429 > >> > >> Fatal error: > >> Atom O in residue CARG 122 not found in rtp entry with 25 atoms > >> while sorting atoms > >> ------------------------------------------------------- > >> > >> > >>> C-terminal carboxylate. > >>> > >>> -Justin > >>> > >>> -- > >>> ======================================== > >>> > >>> Justin A. Lemkul > >>> Ph.D. Candidate > >>> ICTAS Doctoral Scholar > >>> 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://lists.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 gmx-users-requ...@gromacs.org. > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >> > >> > >> > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > 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://lists.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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > > > ------------------------------ > > Message: 4 > Date: Tue, 10 Nov 2009 12:10:57 +0530 (IST) > From: radhika jaswal <jaswalradh...@yahoo.co.in> > Subject: [gmx-users] Please tell me how to simulate two structures > together in a water box > To: gmx-users@gromacs.org > Message-ID: <864176.49303...@web94808.mail.in2.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Respected Sir, > > Please tell me how to simulate two different stuctures together in a > water box so as to have an idea of drug docking and what options to > use. Any suggestions are welcome. > > > > With Regards > > Radhika > > > > > > > Connect more, do more and share more with Yahoo! India Mail. Learn > more. http://in.overview.mail.yahoo.com/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20091110/54378053/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Tue, 10 Nov 2009 12:16:56 +0530 > From: pawan raghav <pwnr...@gmail.com> > Subject: [gmx-users] (no subject) > To: gmx-users@gromacs.org > Message-ID: > <c7ae933b0911092246he5f982fyad982886dfe5c...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > After installing gromacs4.0 on windows it created Gromacs directory > containing several .exe files in bin directory. But when I used pdb2gmx > command it will shows that basch command is not found. So anyone can tell > me > what is that. > > -- > Pawan Kumar Raghav > Bioinformatician > Stem Cell and Gene Therapy Research Group > INMAS, DRDO > Timarpur Delhi-110054 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20091110/57f8cce2/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Tue, 10 Nov 2009 17:59:19 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] (no subject) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4af90f47.8030...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > pawan raghav wrote: > > After installing gromacs4.0 on windows it created Gromacs directory > > containing several .exe files in bin directory. But when I used pdb2gmx > > command it will shows that basch command is not found. So anyone can > > tell me what is that. > > See point 8 here > > http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions > > Mark > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 67, Issue 60 > ***************************************** > -- Pawan Kumar Raghav Bioinformatician Stem Cell and Gene Therapy Research Group INMAS, DRDO Timarpur Delhi-110054
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