[gmx-users] Re: gmx-users Digest, Vol 67, Issue 60
pawan raghav
pwnrghv at gmail.com
Tue Nov 10 09:03:24 CET 2009
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-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
>
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> 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 <js at drugdiscoveryathome.com>
> Subject: Re: [gmx-users] Missing H from residue
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Cc: Andrey Voronkov <av at drugdiscoveryathome.com>
> Message-ID:
> <6c65435e0911091838x89cddeera26061500376e186 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalemkul at 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 at 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-request at 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Missing H from residue
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4AF8D735.1030707 at 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 <jalemkul at 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 at 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-request at 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 <js at drugdiscoveryathome.com>
> Subject: Re: [gmx-users] Missing H from residue
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <6c65435e0911091910r7c932c23l2a2814b72d8be69a at 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 <jalemkul at vt.edu> wrote:
> >
> >
> > Jack Shultz wrote:
> >>
> >> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <jalemkul at 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 at 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-request at 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 at 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-request at 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 <jaswalradhika at yahoo.co.in>
> Subject: [gmx-users] Please tell me how to simulate two structures
> together in a water box
> To: gmx-users at gromacs.org
> Message-ID: <864176.49303.qm at 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/
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> ------------------------------
>
> Message: 5
> Date: Tue, 10 Nov 2009 12:16:56 +0530
> From: pawan raghav <pwnrghv at gmail.com>
> Subject: [gmx-users] (no subject)
> To: gmx-users at gromacs.org
> Message-ID:
> <c7ae933b0911092246he5f982fyad982886dfe5cb6c at 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
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> ------------------------------
>
> Message: 6
> Date: Tue, 10 Nov 2009 17:59:19 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] (no subject)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AF90F47.8030805 at 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 at 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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