[gmx-users] Re: water molecules in vacuum simulation.
anwar at cdfd.org.in
anwar at cdfd.org.in
Wed Sep 27 12:08:52 CEST 2006
Hi all,
I am performing in vacuum simulation of a protein containing crystallographic
water molecules. I want to constrain these water molecules, but pdb2gmx
program doesnot generate the pr.itp for water molecules. How do I constrain
these water molecules.
regards
Anwar
----------------------
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
anwar.m1 at gmail.com
-----------------------
---------REPLY TO-------------
Date:Wed Sep 27 00:30:36 GMT+08:00 2006
FROM: gmx-users-request at gromacs.org
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Subject: gmx-users Digest, Vol 29, Issue 81
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Today's Topics:
1. Re: water molecules in vacuum simulation. (Steffen Wolf)
2. Re: surface tension (Serge Yefimov)
3. Re: EM problem with OPLS and TIP4P (vechism at netscape.net)
4. VAL group (Owen, Michael)
5. distance restraints: -merge (Owen, Michael)
6. Re: Which POPC Bilayer to start? (Jim Fonseca)
----------------------------------------------------------------------
Message: 1
Date: Tue, 26 Sep 2006 12:10:44 +0200
From: Steffen Wolf <swolf at bph.rub.de>
Subject: Re: [gmx-users] water molecules in vacuum simulation.
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4518FCA4.1080305 at bph.rub.de>
Content-Type: text/plain; charset=ISO-8859-1
Hi Anwar,
the answer is: Yes, sure.
CU
Steffen
> Dear users,
> Is it possible to perform an invacuum simulation with few constrained
water
> molecules? I dont want to use the explicit solvent, but want to use the
> crystallographic water molecules in protein and perform invacuum simulation.
> regards
> Anwar
>
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
> -----------------------
>
>
>
> -
>
> _______________________________________________
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--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de
------------------------------
Message: 2
Date: Tue, 26 Sep 2006 11:01:45 +0200
From: Serge Yefimov <s.yefimov at rug.nl>
Subject: Re: [gmx-users] surface tension
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4518EC79.3030407 at rug.nl>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Pri,
Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm)
serge
priyanka srivastava wrote:
> Dear all,
>
> what is the unit of surface tension in gromacs
> analysis? Is it dyn/cm or N/m. As according to me it
> is coming out to be in terms of N/m but it is attached
> with a conversion factor of some powers of 10.
> Kindly guide me. If I am getting e.g. 930.002 as the
> surface tension then what are it's units?
>
> regards,
> Pri...
------------------------------
Message: 3
Date: Tue, 26 Sep 2006 09:22:46 -0400
From: vechism at netscape.net
Subject: Re: [gmx-users] EM problem with OPLS and TIP4P
To: gmx-users at gromacs.org
Message-ID: <8C8AF85FDD3E3A3-1784-373B at FWM-M35.sysops.aol.com>
Content-Type: text/plain; charset="us-ascii"
-----Original Message-----
From: chris.neale at utoronto.ca
To: gmx-users at gromacs.org
Sent: Wed, 20 Sep 2006 10:28 PM
Subject: [gmx-users] EM problem with OPLS and TIP4P
Try this:
unconstrained_start = no
Also ensure that your .top file is correct.
Also take a look at your starting positions, where is MW?
Also ensure that your waters have the correct order:
eg.
871SOL OW 3496 1.935 2.093 1.901
871SOL HW1 3497 1.902 2.172 1.945
871SOL HW2 3498 1.990 2.126 1.830
871SOL MW 3499 1.938 2.107 1.898
The problema was here. In my old tip4p.itp file the water sites were in
reverse order. I just change the order and it works now.
Thanks.
Also try outputting coords for step 20,21,22,23 in the first system and
see what is actually happening.
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Message: 4
Date: Tue, 26 Sep 2006 10:59:08 -0500
From: "Owen, Michael" <MichaelOwen at creighton.edu>
Subject: [gmx-users] VAL group
To: <gmx-users at gromacs.org>
Message-ID:
<80C4D42673F70F4B9333B9F3AFFCC5081D8823 at EXBE06.blue.jays.creighton.edu>
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Hello fellow gmx users,
when I convert a pdb file of a peptide that contains a valyl residue into
a .gro file a separate "group" is made for the atoms in the valyl residue.
This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were
used. The molecule appears as one in the topology file, and the atomic
description of the valyl residue in the pdb file matches that of the ffoplsa.rtp
file.
An excert from the topology file that shows the structure contains one
peptide is below.
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
SOL 6973
An excerpt from my index file that shows the VAL group, with 16 atoms that
are separated from the protein is below:
28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136
28137 28138 28139
28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151
28152 28153 28154
28155 28156 28157 28158 28159 28160 28161 28162
[ VAL ]
154 155 156 157 158 159 160 161 162 163 164 165 166 167 168
169
[ SOL ]
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315
Could something be wrong with the pdb2gmx program?
Thank you in advance for any suggestions.
Sincerely,
Michael Owen
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Message: 5
Date: Tue, 26 Sep 2006 11:10:15 -0500
From: "Owen, Michael" <MichaelOwen at creighton.edu>
Subject: [gmx-users] distance restraints: -merge
To: <gmx-users at gromacs.org>
Message-ID:
<80C4D42673F70F4B9333B9F3AFFCC5081D8824 at EXBE06.blue.jays.creighton.edu>
Content-Type: text/plain; charset="iso-8859-1"
Fellow gmx-users,
I would like to constrain the distance of an ion to specific atoms of a
protein. I recently read a message in which the use of the option -merge
in the pdb2gmx program was suggested. How can I use this option to form
these constraints?
Thank you for your assistance,
Michael Owen
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Message: 6
Date: Tue, 26 Sep 2006 12:18:53 -0400
From: Jim Fonseca <jf163201 at ohiou.edu>
Subject: Re: [gmx-users] Which POPC Bilayer to start?
To: akshay17 at olemiss.edu, Discussion list for GROMACS users
<gmx-users at gromacs.org>
Message-ID: <70FB90EC-756C-4B1E-BBCB-6AA4DD993F3F at ohiou.edu>
Content-Type: text/plain; charset="us-ascii"
I've had success with Tieleman's lipids. I used popc128b.pdb. Since
it has the extra ns of equilibration, I figured it would cause fewer
problems. However, once you start messing around with making hole in
the membrane and adding a protein, you'll need to re-equilibrate
again (EM & PR).
Jim
On Sep 20, 2006, at 5:48 PM, Akshay Patny wrote:
> Hi All
>
> I am trying to use POPC bilayer for doing GPCR simulation.
>
> I have come across two options of generating a POPC bilayer >>>>
>
> 1. I can generate a POPC bilayer from the VMD Membrane plug-in,
> wherein the
> membrane is generated from the pre-built membrane square patches
> and lipid
> tails are (almost) fully extended.
> 2. Alternatively, I can download the pre-equilibrated POPC bilayer
> from Dr.
> Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People
>
> Since, I am new to the GPCR-membrane modeling, can you suggest me
> which out
> of the above two options can be a better starting point for the
> simulation
> of my GPCR protein? A membrane generated from VMD or a pre-
> equilibrated
> membrane?? Would the equilibration time for my protein be lesser in
> one out
> of the two?
>
> If option 2 is a good idea then out of popc128a.pdb and
> popc128b.pdb (both
> available from Prof. Tieleman's website), which will be a better
> model to
> start with?
>
> Thank you very much in advance.
> Akshay
>
> Akshay Patny
>
> Graduate Research Assistant
> Faser Hall 417, Department of Medicinal Chemistry
> Research Institute of Pharmaceutical Sciences
> University of Mississippi
> University, MS 38677
> E-mail: akshay17 at olemiss.edu
> Tel: 662-915-1286 (office); Web: www.olemiss.edu
>
>
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