[gmx-users] Re: Molecular volume
Mohan Boggara
mohanbabu.boggara at gmail.com
Tue Nov 7 00:52:07 CET 2006
Hi David,
Thanks for you reply, g_sas gives solvent accesible surface area but not the
volume. In any case, that might be of some help.
Thanks
Mohan
On 06/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
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> Today's Topics:
>
> 1. Atom q2 not found in rtp database in residue TRP (Joern Lenz)
> 2. Re: Atom q2 not found in rtp database in residue TRP
> (David van der Spoel)
> 3. Smooth surface (Alexei Krukau)
> 4. Re: Atom q2 not found in rtp database in residue TRP (Joern Lenz)
> 5. Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun (Pradip K Biswas)
> 6. Re: (dH/dl) calculation (David Mobley)
> 7. Molecular volume (Mohan Boggara)
> 8. Re: Molecular volume (David Mobley)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 6 Nov 2006 12:03:33 +0100
> From: Joern Lenz <JLenz at zbh.uni-hamburg.de>
> Subject: [gmx-users] Atom q2 not found in rtp database in residue TRP
> To: gmx-users at gromacs.org
> Message-ID: <200611061203.33366.JLenz at zbh.uni-hamburg.de>
> Content-Type: text/plain; charset="us-ascii"
>
> dear gromacs users,
>
> i am performing a simulation of a system of a protein together with a DNA
> using the amber03 forcefield which i loaded down from
> http://folding.stanford.edu/AMBER.html.
> I converted all LYS residues in my pdb file into LYP and all HIS into HIP
> (please correct me if you think that this does not make sense).
> Does anyone know a script or program which automatically converts pdb
> files
> into amber pdb files so that i can use the amber03 FF without changing
> atoms
> here and there ?
>
> QUESTION:
> When i start pdb2gmx there always occurs the same error:
> "Atom q2 not found in rtp database in residue TRP"
> I cannot recognize where this error comes from and so i am not able to fix
> this error.
> Has anyone got an idea ?
> Thanks a lot and have a nice day using gromacs
> greeting
> joern
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 06 Nov 2006 13:39:23 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
> TRP
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <454F2CFB.3050505 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Joern Lenz wrote:
> > dear gromacs users,
> >
> > i am performing a simulation of a system of a protein together with a
> DNA
> > using the amber03 forcefield which i loaded down from
> > http://folding.stanford.edu/AMBER.html.
> > I converted all LYS residues in my pdb file into LYP and all HIS into
> HIP
> > (please correct me if you think that this does not make sense).
> > Does anyone know a script or program which automatically converts pdb
> files
> > into amber pdb files so that i can use the amber03 FF without changing
> atoms
> > here and there ?
> >
> > QUESTION:
> > When i start pdb2gmx there always occurs the same error:
> > "Atom q2 not found in rtp database in residue TRP"
> > I cannot recognize where this error comes from and so i am not able to
> fix
> > this error.
> > Has anyone got an idea ?
>
> check that the columns in your pdb file are correct.
> search for q2 in your pdb file.
>
> > Thanks a lot and have a nice day using gromacs
> > greeting
> > joern
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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
>
>
> --
> 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: Mon, 6 Nov 2006 15:37:42 +0200
> From: Alexei Krukau <alex at heineken.chemie.uni-dortmund.de>
> Subject: [gmx-users] Smooth surface
> To: gmx-users at gromacs.org
> Message-ID: <200611061437.42349.alex at heineken.chemie.uni-dortmund.de>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Gromacs users,
> I would like to ask, if there is a possibility to create a smooth
> (unstructured) hydrophobic or hydrophilic wall in Gromacs?
> --
> Alex Krukau
> Physical Chemistry II a
> University of Dortmund
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 6 Nov 2006 15:15:56 +0100
> From: Joern Lenz <JLenz at zbh.uni-hamburg.de>
> Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
> TRP
> To: gmx-users at gromacs.org
> Message-ID: <200611061515.56099.JLenz at zbh.uni-hamburg.de>
> Content-Type: text/plain; charset="us-ascii"
>
> >>Joern Lenz wrote:
>
> >>dear gromacs users,
>
>
> >>i am performing a simulation of a system of a protein together with a
> DNA
> >>using the amber03 forcefield which i loaded down from
> >>http://folding.stanford.edu/AMBER.html. I converted all LYS residues in
> my
> >>pdb file into LYP and all HIS into HIP (please correct me if you think
> that
> >>this does not make sense). Does anyone know a script or program which
> >>automatically converts pdb files into amber pdb files so that i can use
> the
> >>amber03 FF without changing atoms here and there ?
> >>
> >>
> >>QUESTION: When i start pdb2gmx there always occurs the same error:
> >>"Atom q2 not found in rtp database in residue TRP"
> >>
> >>I cannot recognize where this error comes from and so i am not able to
> fix
> >>this error. Has anyone got an idea ?
>
> >check that the columns in your pdb file are correct.
> >search for q2 in your pdb file.
>
> I checked both suggestions but the error is still there.
> what can i further do to run pdb2gmx correctly ?
> thnaks a lot for ideas.
> Joern
>
> >>Thanks a lot and have a nice day using gromacs
> >>
> >>greetings joern
> >>_______________________________________________
> >>gmx-users mailing list gmx-users at gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-users
> >>
> >>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
>
>
>
> >--
> >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
> >[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >_______________________________________________
> >gmx-users mailing list gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 6 Nov 2006 11:14:11 -0500
> From: Pradip K Biswas <p.biswas at csuohio.edu>
> Subject: [gmx-users] Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun
> To: gmx-users at gromacs.org
> Cc: cseifert at bph.ruhr-uni-bochum.de
> Message-ID:
> <
> OFAE661ABB.57DC1FCE-ON8525721E.00593075-8525721E.00593089 at csuohio.edu>
>
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> ------------------------------
>
> Message: 6
> Date: Mon, 6 Nov 2006 10:19:05 -0800
> From: "David Mobley" <dmobley at gmail.com>
> Subject: Re: [gmx-users] (dH/dl) calculation
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <bc2c99750611061019x38c0fdg24b2c409e81f8c7d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Mauricio,
>
> I'm somewhat confused by your question and notation. However, I think
> the basic answer is something like this: In molecular dynamics, you
> know the Hamiltonian from which you are sampling; call it H(x,p, l),
> where x denotes all of the positions, p the momentums, and l lambda.
> This, of course, is closely linked to the potential energy. Anyway, at
> any snapshot, you can simply take the derivative dH(x,p,l)/dl, and you
> have dH/dl at that snapshot. This is usually straightforward since you
> know the dependence of all of the terms in your Hamiltonian on lambda,
> so you actually have the functional form for dH/dl as well -- so it
> just involves taking the appropriate combination of positions,
> momentums, etc. This is of course all handled internally by the code.
> <dH/dl>, then, is just the time-average of dH/dl, which can be
> evaluated every step by the code.
>
> I am not sure if that's helpful at all, as I'm not entirely sure what
> problem you're having. After all, whenever you do TI calculations in
> GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for every
> snapshot in an xvg output file. Are you just confused about how the
> code gets this (I think I just answered that above), or are you trying
> to figure out how to use it? If you're confused about how to use it,
> try to ask a question that relates to the specific issue you're
> confused about.
>
> Best wishes,
> David Mobley
> UCSF
>
>
> On 11/5/06, Mauricio Sica <msica at unq.edu.ar> wrote:
> > Dear experts
> >
> > I am doing FEP (thermodynamic integration method) simulations.
> > I have a questions about <dH/dl> calculation in GROMACS.
> > Take in mind equation 3.77 from the GROMACS 3.3 manual.
> > There, dA/dl is calculated as
> >
> > dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = <dA/dl>NVT;l }
> >
> > where SS are doble integrals (sorry for the notation).
> >
> > My question is: how is (dH/dl) (in the middel-term of the equation)
> > calculated?
> > My idea is that the difference V(L=1)-V(L=0) is calculated for every
> time
> > step (irrespective of the lambda value of the simulation) and <dG/dl> is
> > the time average of that difference.
> >
> > <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 >
> >
> > Is this correct?
> >
> >
> > Thanks
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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: 7
> Date: Mon, 6 Nov 2006 16:37:58 -0600
> From: "Mohan Boggara" <mohanbabu.boggara at gmail.com>
> Subject: [gmx-users] Molecular volume
> To: gmx-users at gromacs.org
> Message-ID:
> <2fdedacb0611061437u4dac16as1a6879b9c37f7247 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear users,
> Is there a way to calculate molecular volume of small solutes that we use
> in
> simulations?
>
> Mohan
>
> --
> Mohan Boggara
> Graduate Research Assistant
> Dept of Chemical Engineering
> University of Houston
> S222 Engg Bldg 1, 4800 Calhoun Rd,
> Houston, Texas-77204, USA
> Mobile: 1-832-643-5729
> Office: 1-713-743-4314
> http://polymer.chee.uh.edu/
>
> Knowledge is power--unknown
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> ------------------------------
>
> Message: 8
> Date: Mon, 6 Nov 2006 14:58:34 -0800
> From: "David Mobley" <dmobley at gmail.com>
> Subject: Re: [gmx-users] Molecular volume
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <bc2c99750611061458w2eaaf7c0p866dc6c6d19a550 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> I think in 3.3, there was a new option added to g_sas that allows you
> to calculate the solvent accessible volume, which may be what you
> want. Try searching the list.
>
> David
>
>
> On 11/6/06, Mohan Boggara <mohanbabu.boggara at gmail.com> wrote:
> > Dear users,
> > Is there a way to calculate molecular volume of small solutes that we
> use in
> > simulations?
> >
> > Mohan
> >
> > --
> > Mohan Boggara
> > Graduate Research Assistant
> > Dept of Chemical Engineering
> > University of Houston
> > S222 Engg Bldg 1, 4800 Calhoun Rd,
> > Houston, Texas-77204, USA
> > Mobile: 1-832-643-5729
> > Office: 1-713-743-4314
> > http://polymer.chee.uh.edu/
> >
> > Knowledge is power--unknown
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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
> >
> >
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
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>
>
> End of gmx-users Digest, Vol 31, Issue 19
> *****************************************
>
--
Mohan Boggara
Graduate Research Assistant
Dept of Chemical Engineering
University of Houston
S222 Engg Bldg 1, 4800 Calhoun Rd,
Houston, Texas-77204, USA
Mobile: 1-832-643-5729
Office: 1-713-743-4314
http://polymer.chee.uh.edu/
Knowledge is power--unknown
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