Hi David, <br>Thanks for you reply, g_sas gives solvent accesible surface area but not the volume. In any case, that might be of some help. <br>Thanks<br>Mohan <br><br><div><span class="gmail_quote">On 06/11/06, <b class="gmail_sendername">
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br><br>Today's Topics:<br><br> 1. Atom q2 not found in rtp database in residue TRP (Joern Lenz)<br> 2. Re: Atom q2 not found in rtp database in residue TRP<br> (David van der Spoel)<br> 3. Smooth surface (Alexei Krukau)
<br> 4. Re: Atom q2 not found in rtp database in residue TRP (Joern Lenz)<br> 5. Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun (Pradip K Biswas)<br> 6. Re: (dH/dl) calculation (David Mobley)<br> 7. Molecular volume (Mohan Boggara)
<br> 8. Re: Molecular volume (David Mobley)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 6 Nov 2006 12:03:33 +0100<br>From: Joern Lenz <<a href="mailto:JLenz@zbh.uni-hamburg.de">
JLenz@zbh.uni-hamburg.de</a>><br>Subject: [gmx-users] Atom q2 not found in rtp database in residue TRP<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:200611061203.33366.JLenz@zbh.uni-hamburg.de">
200611061203.33366.JLenz@zbh.uni-hamburg.de</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>dear gromacs users,<br><br>i am performing a simulation of a system of a protein together with a DNA<br>
using the amber03 forcefield which i loaded down from<br><a href="http://folding.stanford.edu/AMBER.html">http://folding.stanford.edu/AMBER.html</a>.<br>I converted all LYS residues in my pdb file into LYP and all HIS into HIP
<br>(please correct me if you think that this does not make sense).<br>Does anyone know a script or program which automatically converts pdb files<br>into amber pdb files so that i can use the amber03 FF without changing atoms
<br>here and there ?<br><br>QUESTION:<br>When i start pdb2gmx there always occurs the same error:<br>"Atom q2 not found in rtp database in residue TRP"<br>I cannot recognize where this error comes from and so i am not able to fix
<br>this error.<br>Has anyone got an idea ?<br>Thanks a lot and have a nice day using gromacs<br>greeting<br>joern<br><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 06 Nov 2006 13:39:23 +0100<br>From: David van der Spoel <
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue<br> TRP<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:454F2CFB.3050505@xray.bmc.uu.se">454F2CFB.3050505@xray.bmc.uu.se</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Joern Lenz wrote:
<br>> dear gromacs users,<br>><br>> i am performing a simulation of a system of a protein together with a DNA<br>> using the amber03 forcefield which i loaded down from<br>> <a href="http://folding.stanford.edu/AMBER.html">
http://folding.stanford.edu/AMBER.html</a>.<br>> I converted all LYS residues in my pdb file into LYP and all HIS into HIP<br>> (please correct me if you think that this does not make sense).<br>> Does anyone know a script or program which automatically converts pdb files
<br>> into amber pdb files so that i can use the amber03 FF without changing atoms<br>> here and there ?<br>><br>> QUESTION:<br>> When i start pdb2gmx there always occurs the same error:<br>> "Atom q2 not found in rtp database in residue TRP"
<br>> I cannot recognize where this error comes from and so i am not able to fix<br>> this error.<br>> Has anyone got an idea ?<br><br>check that the columns in your pdb file are correct.<br>search for q2 in your pdb file.
<br><br>> Thanks a lot and have a nice day using gromacs<br>> greeting<br>> joern<br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 6 Nov 2006 15:37:42 +0200
<br>From: Alexei Krukau <<a href="mailto:alex@heineken.chemie.uni-dortmund.de">alex@heineken.chemie.uni-dortmund.de</a>><br>Subject: [gmx-users] Smooth surface<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>Message-ID: <<a href="mailto:200611061437.42349.alex@heineken.chemie.uni-dortmund.de">200611061437.42349.alex@heineken.chemie.uni-dortmund.de</a>><br>Content-Type: text/plain; charset="us-ascii"<br>
<br>Dear Gromacs users,<br>I would like to ask, if there is a possibility to create a smooth<br>(unstructured) hydrophobic or hydrophilic wall in Gromacs?<br>--<br>Alex Krukau<br>Physical Chemistry II a<br>University of Dortmund
<br><br><br>------------------------------<br><br>Message: 4<br>Date: Mon, 6 Nov 2006 15:15:56 +0100<br>From: Joern Lenz <<a href="mailto:JLenz@zbh.uni-hamburg.de">JLenz@zbh.uni-hamburg.de</a>><br>Subject: Re: [gmx-users] Atom q2 not found in rtp database in residue
<br> TRP<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:200611061515.56099.JLenz@zbh.uni-hamburg.de">200611061515.56099.JLenz@zbh.uni-hamburg.de</a>><br>
Content-Type: text/plain; charset="us-ascii"<br><br>>>Joern Lenz wrote:<br><br>>>dear gromacs users,<br><br><br>>>i am performing a simulation of a system of a protein together with a DNA<br>>>using the amber03 forcefield which i loaded down from
<br>>><a href="http://folding.stanford.edu/AMBER.html">http://folding.stanford.edu/AMBER.html</a>. I converted all LYS residues in my<br>>>pdb file into LYP and all HIS into HIP (please correct me if you think that
<br>>>this does not make sense). Does anyone know a script or program which<br>>>automatically converts pdb files into amber pdb files so that i can use the<br>>>amber03 FF without changing atoms here and there ?
<br>>><br>>><br>>>QUESTION: When i start pdb2gmx there always occurs the same error:<br>>>"Atom q2 not found in rtp database in residue TRP"<br>>><br>>>I cannot recognize where this error comes from and so i am not able to fix
<br>>>this error. Has anyone got an idea ?<br><br>>check that the columns in your pdb file are correct.<br>>search for q2 in your pdb file.<br><br>I checked both suggestions but the error is still there.<br>what can i further do to run pdb2gmx correctly ?
<br>thnaks a lot for ideas.<br>Joern<br><br>>>Thanks a lot and have a nice day using gromacs<br>>><br>>>greetings joern<br>>>_______________________________________________<br>>>gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>><br>>>Please don't post (un)subscribe requests to the list. Use the www interface
<br>>>or send it to [EMAIL PROTECTED]<br>>>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br><br>>--<br>>David.<br>>________________________________________________________________________
<br>>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>>Dept. of Cell and Molecular Biology, Uppsala University.<br>>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>>phone: 46 18 471 4205 fax: 46 18 511 755
<br>>[EMAIL PROTECTED] [EMAIL PROTECTED] <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>>_______________________________________________
<br>>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
<br><br>------------------------------<br><br>Message: 5<br>Date: Mon, 6 Nov 2006 11:14:11 -0500<br>From: Pradip K Biswas <<a href="mailto:p.biswas@csuohio.edu">p.biswas@csuohio.edu</a>><br>Subject: [gmx-users] Re: Fw:
gmx-3.3.1_cpmd-3.11.1 with mpirun<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Cc: <a href="mailto:cseifert@bph.ruhr-uni-bochum.de">cseifert@bph.ruhr-uni-bochum.de</a><br>Message-ID:<br> <
<a href="mailto:OFAE661ABB.57DC1FCE-ON8525721E.00593075-8525721E.00593089@csuohio.edu">OFAE661ABB.57DC1FCE-ON8525721E.00593075-8525721E.00593089@csuohio.edu</a>><br><br>Content-Type: text/plain; charset="us-ascii"
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</a><br><br>------------------------------<br><br>Message: 6<br>Date: Mon, 6 Nov 2006 10:19:05 -0800<br>From: "David Mobley" <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>><br>Subject: Re: [gmx-users] (dH/dl) calculation
<br>To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a href="mailto:bc2c99750611061019x38c0fdg24b2c409e81f8c7d@mail.gmail.com">
bc2c99750611061019x38c0fdg24b2c409e81f8c7d@mail.gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Mauricio,<br><br>I'm somewhat confused by your question and notation. However, I think
<br>the basic answer is something like this: In molecular dynamics, you<br>know the Hamiltonian from which you are sampling; call it H(x,p, l),<br>where x denotes all of the positions, p the momentums, and l lambda.<br>This, of course, is closely linked to the potential energy. Anyway, at
<br>any snapshot, you can simply take the derivative dH(x,p,l)/dl, and you<br>have dH/dl at that snapshot. This is usually straightforward since you<br>know the dependence of all of the terms in your Hamiltonian on lambda,
<br>so you actually have the functional form for dH/dl as well -- so it<br>just involves taking the appropriate combination of positions,<br>momentums, etc. This is of course all handled internally by the code.<br><dH/dl>, then, is just the time-average of dH/dl, which can be
<br>evaluated every step by the code.<br><br>I am not sure if that's helpful at all, as I'm not entirely sure what<br>problem you're having. After all, whenever you do TI calculations in<br>GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for every
<br>snapshot in an xvg output file. Are you just confused about how the<br>code gets this (I think I just answered that above), or are you trying<br>to figure out how to use it? If you're confused about how to use it,<br>
try to ask a question that relates to the specific issue you're<br>confused about.<br><br>Best wishes,<br>David Mobley<br>UCSF<br><br><br>On 11/5/06, Mauricio Sica <<a href="mailto:msica@unq.edu.ar">msica@unq.edu.ar</a>
> wrote:<br>> Dear experts<br>><br>> I am doing FEP (thermodynamic integration method) simulations.<br>> I have a questions about <dH/dl> calculation in GROMACS.<br>> Take in mind equation 3.77 from the GROMACS
3.3 manual.<br>> There, dA/dl is calculated as<br>><br>> dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = <dA/dl>NVT;l }<br>><br>> where SS are doble integrals (sorry for the notation).<br>><br>
> My question is: how is (dH/dl) (in the middel-term of the equation)<br>> calculated?<br>> My idea is that the difference V(L=1)-V(L=0) is calculated for every time<br>> step (irrespective of the lambda value of the simulation) and <dG/dl> is
<br>> the time average of that difference.<br>><br>> <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 ><br>><br>> Is this correct?<br>><br>><br>> Thanks<br>><br>><br>><br>> _______________________________________________
<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br>------------------------------<br><br>Message: 7<br>Date: Mon, 6 Nov 2006 16:37:58 -0600<br>From: "Mohan Boggara" <<a href="mailto:mohanbabu.boggara@gmail.com">
mohanbabu.boggara@gmail.com</a>><br>Subject: [gmx-users] Molecular volume<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a href="mailto:2fdedacb0611061437u4dac16as1a6879b9c37f7247@mail.gmail.com">
2fdedacb0611061437u4dac16as1a6879b9c37f7247@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear users,<br>Is there a way to calculate molecular volume of small solutes that we use in
<br>simulations?<br><br>Mohan<br><br>--<br>Mohan Boggara<br>Graduate Research Assistant<br>Dept of Chemical Engineering<br>University of Houston<br>S222 Engg Bldg 1, 4800 Calhoun Rd,<br>Houston, Texas-77204, USA<br>Mobile: 1-832-643-5729
<br>Office: 1-713-743-4314<br><a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/</a><br><br>Knowledge is power--unknown<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL:
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<br><br>Message: 8<br>Date: Mon, 6 Nov 2006 14:58:34 -0800<br>From: "David Mobley" <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>><br>Subject: Re: [gmx-users] Molecular volume<br>To: "Discussion list for GROMACS users" <
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a href="mailto:bc2c99750611061458w2eaaf7c0p866dc6c6d19a550@mail.gmail.com">bc2c99750611061458w2eaaf7c0p866dc6c6d19a550@mail.gmail.com
</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>I think in 3.3, there was a new option added to g_sas that allows you<br>to calculate the solvent accessible volume, which may be what you<br>
want. Try searching the list.<br><br>David<br><br><br>On 11/6/06, Mohan Boggara <<a href="mailto:mohanbabu.boggara@gmail.com">mohanbabu.boggara@gmail.com</a>> wrote:<br>> Dear users,<br>> Is there a way to calculate molecular volume of small solutes that we use in
<br>> simulations?<br>><br>> Mohan<br>><br>> --<br>> Mohan Boggara<br>> Graduate Research Assistant<br>> Dept of Chemical Engineering<br>> University of Houston<br>> S222 Engg Bldg 1, 4800 Calhoun Rd,
<br>> Houston, Texas-77204, USA<br>> Mobile: 1-832-643-5729<br>> Office: 1-713-743-4314<br>> <a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/</a><br>><br>> Knowledge is power--unknown<br>
> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<br>
> <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>><br><br><br>------------------------------<br><br>_______________________________________________
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End of gmx-users Digest, Vol 31, Issue 19<br>*****************************************<br></blockquote></div><br><br clear="all"><br>-- <br>Mohan Boggara<br>Graduate Research Assistant<br>Dept of Chemical Engineering<br>University of Houston
<br>S222 Engg Bldg 1, 4800 Calhoun Rd,<br>Houston, Texas-77204, USA<br>Mobile: 1-832-643-5729<br>Office: 1-713-743-4314 <br><a href="http://polymer.chee.uh.edu/">http://polymer.chee.uh.edu/</a><br><br>Knowledge is power--unknown