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 [EMAIL PROTECTED] ----------------------- ---------REPLY TO------------- Date:Wed Sep 27 00:30:36 GMT+08:00 2006 FROM: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 29, Issue 81 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." 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 ([EMAIL PROTECTED]) 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 <[EMAIL PROTECTED]> Subject: Re: [gmx-users] water molecules in vacuum simulation. To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] > ----------------------- > > > > - > > _______________________________________________ > 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 > -- 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: [EMAIL PROTECTED] Web: http://www.bph.rub.de ------------------------------ Message: 2 Date: Tue, 26 Sep 2006 11:01:45 +0200 From: Serge Yefimov <[EMAIL PROTECTED]> Subject: Re: [gmx-users] surface tension To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] Subject: Re: [gmx-users] EM problem with OPLS and TIP4P To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" -----Original Message----- From: [EMAIL PROTECTED] To: gmx-users@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. _______________________________________________ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/1a93ad45/attachment-0001.html ------------------------------ Message: 4 Date: Tue, 26 Sep 2006 10:59:08 -0500 From: "Owen, Michael" <[EMAIL PROTECTED]> Subject: [gmx-users] VAL group To: <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/d17613e0/attachment-0001.html ------------------------------ Message: 5 Date: Tue, 26 Sep 2006 11:10:15 -0500 From: "Owen, Michael" <[EMAIL PROTECTED]> Subject: [gmx-users] distance restraints: -merge To: <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060926/3433c22c/attachment-0001.html ------------------------------ Message: 6 Date: Tue, 26 Sep 2006 12:18:53 -0400 From: Jim Fonseca <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Which POPC Bilayer to start? To: [EMAIL PROTECTED], Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] > Tel: 662-915-1286 (office); Web: www.olemiss.edu > > > _______________________________________________ > 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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