[gmx-users] Prot_prep_query

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 11 22:11:37 CEST 2007


Hi Prasenjit,

First, please don't include a whole digest into your reply :S What a
scroll down.

Did pdb2gmx say anything when not giving hydrogen atoms? It sounds
weird that they were added in the .top but not in the .itp. Maybe
first clean the directory, such that you only have the original .pdb
and run pdb2gmx with -ignh but without -inter. If you find that the
output .pdb/.gro file doesn't have the hydrogens in, but the .top file
does, please report back exactly what command you gave, which force
field, which operating system and which shoe size you have. Well, you
can leave the latter. The output of pdb2gmx might come in handy.

Best,

Tsjerk

On 4/11/07, pkmukher <pkmukher at olemiss.edu> wrote:
> Hello Andrea,
>
>    Thanks for your reply. Actually I am not doing a NMR
> constraint based refinement of the structure. Its a NMR
> derived ligand-protein complex submitted in the pdb. I want
> to prepare the complex using the tutorial. In the tutorial
> they have a crystal structure without hydrogens. Since in my
> case I had hydrogens present and it was interfering with the
> preparation using gromos ff i thought of stripping the
> hydrogens and re adding them. I thought of using the -inter
> flag to control the protonation of key residue types. My
> problem is that when used the stripped pdb in the second
> stage the output pdb file does not write the hydrogens while
> the top file does. Since the next step will be to add the
> ligand coordinates(polar hydrogens added) I should also have
> a protein pdb structure with polar hydrogens added.Thanks
>
> **In case you need to refer to the previous mail
>
> Hello gromacs users,
>
>
>   I am facing a particular problem in the preparation of my
> protein.I have a NMR derived structure with hydrogens. To
> prepare my protein i thought of a two step procedure
> 1)stripping the protein of the hydrogens using -ignh and
> saving pdb output
> 2)submitting the pdb output file from stage 1 using the
> -inter flag to get my final .top .gro and .pdb files
>
> I find that at the end of step 1 the pdb output is stripped
> of hydrogens.
> In the second stage I find that the .top file has the
> hydrogens listed (only polar hydrogens) but the pdb output
> is still without any hydrogens.
>
> I want to follow the gromacs tutorial titled
> GROMACS Tutorial for Drug – Enzyme Complex.
> http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
>
> here they have used a prepared protein pdb file while
> merging the ligand coordinates to form the final complex.
>
> My questions are
>
> 1) why the pdb file written in step two does not contain the
> hydrogens and how can i solve this issue?
>
> 2) Is there any other way to prepare the ligand-protein
> complex without using the protein .pdb output?
>
> 3) This is a slightly unrelated question. Could some body
> guide me to any tutorials etc where they have shown how to
> calculate gausssian charges for the ligand and then
> incorporate into the gromacs ligand file?
>
> I can provide the protein structure file. I couldnt load it
> to the group mail because of size limitations
>
> Thanking you in anticipation
>
> > Send gmx-users mailing list submissions to
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> > When replying, please edit your Subject line so it is more
> > specific than "Re: Contents of gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: overcome the integration problem (installing
> > CVS) (Yang Ye)
> >    2. Re: overcome the integration problem (installing
> > CVS)
> >       (David van der Spoel)
> >    3. Re: question about the total-energy of energy
> > minimization
> >       (Mark Abraham)
> >    4. Hi all (ann rose)
> >    5. Re: overcome the integration problem (installing
> > CVS) (Berk Hess)
> >    6. Re: Hi all (Mark Abraham)
> >    7. Prot_prep_problem (pkmukher)
> >    8. Re: Prot_prep_problem (andrea spitaleri)
> >
> >
> > ----------------------------------------------------------
> > ------------
> >
> > Message: 1
> > Date: Wed, 11 Apr 2007 18:07:19 +0800
> > From: Yang Ye <leafyoung81-group at yahoo.com>
> > Subject: Re: [gmx-users] overcome the integration problem
> > (installing
> >     CVS)
> > To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org> Message-ID:
> > <461CB357.4060307 at yahoo.com> Content-Type: text/plain;
> > charset=ISO-8859-1; format=flowed
> >
> >
> >
> > On 4/11/2007 5:52 PM, Dr Itamar Kass wrote:
> > > Shalom all,
> > >
> > > To my best understanding, there is a correction to the
> > > single precision integration problem ("A common,
> > > avoidable source of error in molecular dynamics
> > > integrators" J. Chem. Phys. 126, 046101 (2007).) at the
> > CVS. >
> > > I want to know were can I get it and how to install it.
> > > First, the GROMACS site is down now. Second from the bit
> > > I have read, it is not clear to me how to install the
> > stable CVS and not an experimentally version. >
> > >
> > Stable version:
> > cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs
> > login cvs -z3 -d
> > :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co -r
> > release-3-3-patches gmx
> >
> > HEAD Branch
> > cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs
> > login cvs -z3 -d
> > :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co gmx
> >
> > > Best,
> > > Itamar
> > >
> > > ---
> > >
> > > "Prediction is very difficult, especially about the
> > future" - Niels Bohr >
> > >
> ===========================================
> > > | Itamar Kass, Ph.D.
> > > | Postdoctoral Research Fellow
> > > |
> > > |Molecular Dynamics Group
> > > | School of Molecular and Microbial Sciences (SMMS)
> > > | Chemistry Building (#68)
> > > | The University of Queensland
> > > | St. Lucia Campus, Brisbane, QLD 4067
> > > | Australia
> > > |
> > > | Tel: +61 7 3365 9922
> > > | Fax: +61 7 3365 3872
> > > | E-mail: ikass at uq.edu.au
> > > | Web page: http://www.uq.edu.au/~uqikass/
> > > | Personal web page: http://thekassfamily.blogspot.com/
> > >
> ============================================
> > >
> > > Unless stated otherwise, this e-mail represents only the
> > > views of the Sender and not the views of The University
> > of Queensland >
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at 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
> > gmx-users-request at gromacs.org. Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php >
> > >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 11 Apr 2007 12:13:13 +0200
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] overcome the integration problem
> > (installing
> >     CVS)
> > To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org> Message-ID:
> > <461CB4B9.30103 at xray.bmc.uu.se> Content-Type: text/plain;
> > charset=ISO-8859-1; format=flowed
> >
> > Yang Ye wrote:
> > >
> > >
> > > On 4/11/2007 5:52 PM, Dr Itamar Kass wrote:
> > >> Shalom all,
> > >>
> > >> To my best understanding, there is a correction to the
> > single precision >> integration problem ("A common,
> > avoidable source of error in molecular >> dynamics
> > integrators" >> J. Chem. Phys. 126, 046101 (2007).) at the
> > CVS. >>
> > >> I want to know were can I get it and how to install it.
> > First, the >> GROMACS site is down now. Second from the
> > bit I have read, it is not >> clear to me how to install
> > the stable CVS and not an experimentally  >> version.
> > >>
> > >>
> > > Stable version:
> > > cvs -z3 -d
> > > :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login cvs
> > -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co
> > > -r  release-3-3-patches gmx
> > >
> > > HEAD Branch
> > > cvs -z3 -d
> > > :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login cvs
> > -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co
> > > gmx
> > >> Best,
> > >> Itamar
> > >>
> > The stable version does not have the fix (because it will
> > change results).
> >
> > --
> > David.
> > __________________________________________________________
> > ______________ David van der Spoel, PhD, Assoc. Prof.,
> > Molecular Biophysics group, Dept. of Cell and Molecular
> > Biology, Uppsala University. Husargatan 3, Box 596,
> > 75124 Uppsala, Sweden phone:    46 18 471 4205        fax:
> > 46 18 511 755 spoel at xray.bmc.uu.se    spoel at gromacs.org
> > http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ++++++++++++++
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Wed, 11 Apr 2007 21:14:55 +1000
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] question about the total-energy
> > of energy
> >     minimization
> > To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org> Message-ID:
> > <461CC32F.2030103 at anu.edu.au> Content-Type: text/plain;
> > charset=ISO-8859-1; format=flowed
> >
> > Qiao Baofu wrote:
> > > Hi all,
> > >
> > > I run an energy minization, then calculated the energy,
> > > obtained the  following results:
> > >
> > > LJ-(SR)                    -4431.62    1905.29
> > > 1886.7     -27.08    -919.923
> > > Coulomb-(SR)          - 35926.5    14398.4    14389.9
> > > -50.5129   -1715.95 Potential                  -46818.1
> > >   20524.5    20248.7    -341.91    -11614.9
> > > Kinetic-En.                       0          0
> > > 0           0          0
> > > Total-Energy                     0          0          0
> > >           0          0
> > > Temperature                     0          0          0
> > >          0          0
> > >
> > > Why the Total-energy is not the sum of Potential and
> > Kinetic-En.?  Thanks!
> >
> > In a minimization, you have no kinetic energy. Thus the
> > potential energy  is the total energy and nobody bothered
> > copying over the value.
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Wed, 11 Apr 2007 13:39:45 +0200
> > From: "ann rose" <annrose.johns at gmail.com>
> > Subject: [gmx-users] Hi all
> > To: gmx-users at gromacs.org
> > Message-ID:
> >
> > <4336b97b0704110439s42ead549o22c14167fc5afe1a at mail.gmail.c
> > om> Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi
> >
> > I am new to Gromacs.
> > I would like to simulate oligoether branched polysiloxanes
> > in gromacs. I have the force field availble for the same
> > Whether gromacs will support force filed for polymers
> > containing hetreo atmos like silicon?
> > If so how can I incoroprate this into gromacs?
> > and also
> > How to get the starting configuration for the
> > poysiloxanes? ( like .gro, ..top, .itp files)
> > top, .itp files)
> >
> > Thanking you in advance
> >
> > ann
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://www.gromacs.org/pipermail/gmx-users/attachments/20070411/05362ed7/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Wed, 11 Apr 2007 13:40:50 +0200
> > From: "Berk Hess" <gmx3 at hotmail.com>
> > Subject: Re: [gmx-users] overcome the integration problem
> > (installing
> >     CVS)
> > To: gmx-users at gromacs.org
> > Message-ID: <BAY110-F21BD4D6E1FC70F6E38F1EC8E5F0 at phx.gbl>
> > Content-Type: text/plain; format=flowed
> >
> >
> >
> >
> > >From: David van der Spoel <spoel at xray.bmc.uu.se>
> > >Reply-To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org> >To: Discussion list for GROMACS
> > users <gmx-users at gromacs.org> >Subject: Re: [gmx-users]
> > overcome the integration problem (installing CVS) >Date:
> > Wed, 11 Apr 2007 12:13:13 +0200 >
> > >Yang Ye wrote:
> > >>
> > >>
> > >>On 4/11/2007 5:52 PM, Dr Itamar Kass wrote:
> > >>>Shalom all,
> > >>>
> > >>>To my best understanding, there is a correction to the
> > single precision >>>integration problem ("A common,
> > avoidable source of error in molecular >>>dynamics
> > integrators" >>>J. Chem. Phys. 126, 046101 (2007).) at the
> > CVS. >>>
> > >>>I want to know were can I get it and how to install it.
> > First, the >>>GROMACS site is down now. Second from the
> > bit I have read, it is not >>>clear to me how to install
> > the stable CVS and not an experimentally  >>>version.
> > >>>
> > >>>
> > >>Stable version:
> > >>cvs -z3 -d
> > :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login >>cvs
> > -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co
> > -r  >>release-3-3-patches gmx
> > >>
> > >>HEAD Branch
> > >>cvs -z3 -d
> > :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login >>cvs
> > -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co
> > gmx >>
> > >>>Best,
> > >>>Itamar
> > >>>
> > >The stable version does not have the fix (because it will
> > change results). >
> > >--
> > >David.
> >
> > I would like to add that for a constant temperature
> > ensemble the effect of this fix is neglegible.
> > It is only useful for constant NVE simulations.
> >
> > Berk.
> >
> > __________________________________________________________
> > _______ Play online games with your friends with Messenger
> > http://www.join.msn.com/messenger/overview
> >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Wed, 11 Apr 2007 21:48:16 +1000
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] Hi all
> > To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org> Message-ID:
> > <461CCB00.7000009 at anu.edu.au> Content-Type: text/plain;
> > charset=ISO-8859-1; format=flowed
> >
> > ann rose wrote:
> > > Hi
> > >
> > > I am new to Gromacs.
> > > I would like to simulate oligoether branched
> > > polysiloxanes in gromacs. I  have the force field
> > > availble for the same Whether gromacs will support force
> > > filed for polymers containing hetreo  atmos like
> > silicon?
> >
> > Yes - this information is part of the force field.
> >
> > > If so how can I incoroprate this into gromacs?
> >
> > You will need a thorough working knowledge of at least
> > chapter 5 of the  manual, and plenty from earlier
> > sections. This will also let you assess  whether the range
> > of functions computed by gromacs is suitable for your
> > forcefield.
> >
> > > and also
> > > How to get the starting configuration for the
> > > poysiloxanes? ( like .gro,  .top, .itp files)
> >
> > .gro files are structure files... you're responsible for
> > generating  .gro files are structure files... you're
> > responsible for generating  them. Search the mailing list
> > for suggestions.
> >
> > .top files can be generated by pdb2gmx if you can generate
> > suitable .rtp  .top files can be generated by pdb2gmx if
> > you can generate suitable .rtp  monomers, but life may be
> > messy here for branched polymers... you may  need to make
> > these by hand.
> >
> > .itp files are included by .top files and include your
> > basic force field  .itp files are included by .top files
> > and include your basic force field  files as well as
> > regularly recycled units like solvents... you need to
> > make these.
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Wed, 11 Apr 2007 09:44:45 -0500
> > From: "pkmukher" <pkmukher at olemiss.edu>
> > Subject: [gmx-users] Prot_prep_problem
> > To: gmx-users at gromacs.org
> > Message-ID: <461cf45d.22f.3258.32102 at olemiss.edu>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hello gromacs users,
> >
> >
> >   I am facing a particular problem in the preparation of
> > my protein.I have a NMR derived structure with hydrogens.
> > To prepare my protein i thought of a two step procedure
> > 1)stripping the protein of the hydrogens using -ignh and
> > saving pdb output
> > 2)submitting the pdb output file from stage 1 using the
> > -inter flag to get my final .top .gro and .pdb files
> >
> > I find that at the end of step 1 the pdb output is
> > stripped of hydrogens.
> > In the second stage I find that the .top file has the
> > hydrogens listed (only polar hydrogens) but the pdb output
> > is still without any hydrogens.
> >
> > I want to follow the gromacs tutorial titled
> > GROMACS Tutorial for Drug – Enzyme Complex.
> >
> http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
> >
> > here they have used a prepared protein pdb file while
> > merging the ligand coordinates to form the final complex.
> >
> > My questions are
> >
> > 1) why the pdb file written in step two does not contain
> > the hydrogens and how can i solve this issue?
> >
> > 2) Is there any other way to prepare the ligand-protein
> > complex without using the protein .pdb output?
> >
> > 3) This is a slightly unrelated question. Could some body
> > guide me to any tutorials etc where they have shown how to
> > calculate gausssian charges for the ligand and then
> > incorporate into the gromacs ligand file?
> >
> > I can provide the protein structure file. I couldnt load
> > it to the group mail because of size limitations
> >
> > Thanking you in anticipation
> >
> > Prasenjit Kumar Mukherjee
> > Graduate Student
> > Department of Medicinal Chemistry
> > School of Pharmacy
> > University of Mississippi
> > USA
> >
> > Cell   - 662 380 0146
> > Office - 662 915 1286
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Wed, 11 Apr 2007 16:52:26 +0200
> > From: andrea spitaleri <spitaleri.andrea at hsr.it>
> > Subject: Re: [gmx-users] Prot_prep_problem
> > To: Discussion list for GROMACS users
> > <gmx-users at gromacs.org> Message-ID:
> > <461CF62A.1060109 at hsr.it> Content-Type: text/plain;
> > charset=UTF-8
> >
> > HI Pkmukher,
> > I use to use opls for nmr structures in order to keep the
> > all-hydrogen in the protein and ligand too. However if you
> > want to be sticked with gromos ff I do as follow: 1.
> > prepare my system with -ignh option in pdb2gmx 2. run the
> > simulation 3. use protonate over the pdb and the final trr
> > in order to analyze for instance the violated NOE. Skip
> > last question, sorry :)
> >
> > Regards
> >
> > andrea
> >
> > pkmukher wrote:
> > > Hello gromacs users,
> > >
> > >
> > >   I am facing a particular problem in the preparation of
> > > my protein.I have a NMR derived structure with
> > > hydrogens. To prepare my protein i thought of a two step
> > > procedure 1)stripping the protein of the hydrogens using
> > > -ignh and saving pdb output
> > > 2)submitting the pdb output file from stage 1 using the
> > > -inter flag to get my final .top .gro and .pdb files
> > >
> > > I find that at the end of step 1 the pdb output is
> > > stripped of hydrogens.
> > > In the second stage I find that the .top file has the
> > > hydrogens listed (only polar hydrogens) but the pdb
> > > output is still without any hydrogens.
> > >
> > > I want to follow the gromacs tutorial titled
> > > GROMACS Tutorial for Drug â€" Enzyme Complex.
> > >
> >
> http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
> > >
> > > here they have used a prepared protein pdb file while
> > > merging the ligand coordinates to form the final
> > > complex.
> > > My questions are
> > >
> > > 1) why the pdb file written in step two does not contain
> > > the hydrogens and how can i solve this issue?
> > >
> > > 2) Is there any other way to prepare the ligand-protein
> > > complex without using the protein .pdb output?
> > >
> > > 3) This is a slightly unrelated question. Could some
> > > body guide me to any tutorials etc where they have shown
> > > how to calculate gausssian charges for the ligand and
> > > then incorporate into the gromacs ligand file?
> > >
> > > I can provide the protein structure file. I couldnt load
> > > it to the group mail because of size limitations
> > >
> > > Thanking you in anticipation
> > >
> > > Prasenjit Kumar Mukherjee
> > > Graduate Student
> > > Department of Medicinal Chemistry
> > > School of Pharmacy
> > > University of Mississippi
> > > USA
> > >
> > > Cell   - 662 380 0146
> > > Office - 662 915 1286
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at 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
> > gmx-users-request at gromacs.org. Can't post? Read
> > > http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > -------------------------------
> > Andrea Spitaleri PhD
> > Dulbecco Telethon Institute
> > c/o DIBIT Scientific Institute
> > Biomolecular NMR, 1B4
> > Via Olgettina 58
> > 20132 Milano (Italy)
> > http://biomolecularnmr.ihsr.dom/
> > -------------------------------
> >
> > **********************************************************
> > ********** Sostieni la ricerca del San Raffaele con il
> > 5permille! E' SEMPLICE E NON COSTA NULLA.
> > Basta indicare nell'apposito riquadro della dichiarazione
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> > Fondazione Centro S. Raffaele del Monte Tabor:
> > 03 06 42 80 153 e ricordarsi di firmare.
> > Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai
> > sul sito www.5xmille.org
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search
> > before posting!
> >
> > End of gmx-users Digest, Vol 36, Issue 28
> > *****************************************
> >
> >
>
> Prasenjit Kumar Mukherjee
> Graduate Student
> Department of Medicinal Chemistry
> School of Pharmacy
> University of Mississippi
> USA
>
> Cell   - 662 380 0146
> Office - 662 915 1286
>
>
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



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