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,
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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 < [EMAIL PROTECTED]>
Subject: [gmx-users] Atom q2 not found in rtp database in residue TRP
To: gmx-users@gromacs.org
Message-ID: < [EMAIL PROTECTED]>
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 < [EMAIL PROTECTED]>
Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
TRP
To: Discussion list for GROMACS users < gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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@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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 3
Date: Mon, 6 Nov 2006 15:37:42 +0200
From: Alexei Krukau <[EMAIL PROTECTED]>
Subject: [gmx-users] Smooth surface
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
TRP
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
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@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@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 <[EMAIL PROTECTED]>
Subject: [gmx-users] Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun
To: gmx-users@gromacs.org
Cc: [EMAIL PROTECTED]
Message-ID:
< [EMAIL PROTECTED]>
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------------------------------
Message: 6
Date: Mon, 6 Nov 2006 10:19:05 -0800
From: "David Mobley" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] (dH/dl) calculation
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
< [EMAIL PROTECTED]>
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 <[EMAIL PROTECTED] > 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@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
>
------------------------------
Message: 7
Date: Mon, 6 Nov 2006 16:37:58 -0600
From: "Mohan Boggara" < [EMAIL PROTECTED]>
Subject: [gmx-users] Molecular volume
To: gmx-users@gromacs.org
Message-ID:
< [EMAIL PROTECTED]>
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" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Molecular volume
To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED] >
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 <[EMAIL PROTECTED]> 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@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
>
>
------------------------------
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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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