Re: [gmx-users] How to restrain dihedral angles to reserve the tacticity?

Hello I think constraining rotation about all the main chain bonds should be sufficient to preserve the tacticity. So taking your example, the dihedral angles could be R1 C1 C2 C1 and C1 C2 C1 R2. Of course you will have restrain all similar dihedral angles along the whole length of your polymer.

Re: [gmx-users] Re: How to restrain dihedral angles to reserve the tacticity?

Dear Acharya, Thank you very much for this quick reply. According to your suggestion, I measure the main chain dihedral angles, only to find that same values are obtained for both isotactic and syndiotactic ones. That is obvious i think for a correct tacticity polymeric chain. Therefore, this

Re: [gmx-users] error after grompp

in the gromacs manual. In essence, defining different coupling groups allows control over the temperature of the Groups especially protein and water which otherwise have been seen to differ in the temperature attained by a large degree. Cheers Abhishek Acharya Structural and Computational Biology

Re: [gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)

of the box length in the particular direction. That is what the error is all about. So if you need to pull in all three directions by a particular distance, then make sure that the box length in all directions are greater than twice the pull distance. Cheers Abhishek Acharya Structural

Re: [gmx-users] ATP/Mg+2 parameters

Hello George, You need to use Antechamber, a software provided by the amber developers in a free Amber Tools package. That will produce the right parameters for the Amber force feild. Cheers Abhishek Hello Joao Thanks for the reply; I am planning to use Amber 99SB-ILDN force field. I just

Re: [gmx-users] genion doesn't work in 4.6.1?

and CL ions to neutralize the charge and sufficiently reach the given conc., in this case 0.15 M) Cheers. Abhishek Acharya Structural and Computational Biology Lab Indian Institute of Technology Kanpur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

RE: [gmx-users] genion doesn't work in 4.6.1?

Again and again posting from Abhishek Acharya or Shima, or Rama David or somehow else ... pls read my posting before, it could be useful for you, Indian fellows ... maybe it's possible to get some kind of agreement though brahmin.net or so .. Best regards of somebody experienced with Indian

[gmx-users] High Temperatures in NVT

. rmsd 1.95652e+03 -2.24892e+021.49190e+042.42873e-05 With Regards Abhishek Acharya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] High Temperatures in NVT

fit... :-) Mark On Fri, Mar 15, 2013 at 7:48 AM, Abhishek Acharya aacha...@iitk.ac.inwrote: Hello Gromacs Users. I ran an NVT simulation and i noticed that after the initial step at 300K the temperature shoots up to order of 10^3 and then suddenly comes down around 300K. Is there something

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

the same error. In any case, gromacs4.6 got installed properly by disabling shared libraries and is up and running. Though i would be interested in knowing if its possible to remove this error in any other way. with regards Abhishek On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya aacha

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

the right MPI wrapper compiler) might cause symptoms like yours, we need more complete information to have a chance of helping solve your problem. Christoph also asked for your cmake command line. Mark On Mon, Mar 4, 2013 at 9:04 PM, Abhishek Acharya aacha...@iitk.ac.inwrote: OK

[gmx-users] Installation Problems with Gromacs4.6

such problems. I need 4.6 because my tpr files are produced in Gromacs4.6 and I am using the Verlet cutoff scheme. Thanks in advance With Regards Abhishek Acharya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

Date: Fri, 1 Mar 2013 23:59:36 +0530 From: Abhishek Acharya aacha...@iitk.ac.in Subject: [gmx-users] Installation Problems with Gromacs4.6 To: gromacs maillist gmx-users@gromacs.org Message-ID: 2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in Content-Type: text/plain

Re: [gmx-users][Solved] Removing errors related to missing dihedrals.

/13 4:15 PM, Abhishek Acharya wrote: Hello Justin Thank you very much for your effort and help. I will try adding new parameter corresponding to the errors. Meanwhile just out of curiosity and possible need, what should be done in case no matching parameters are found for the missing

[gmx-users] General query regarding MD simulation.

With Regards Abhishek Acharya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] General query regarding MD simulation.

On 2/15/13 1:29 PM, Abhishek Acharya wrote: Dear GROMACS Users. Just out of curiosity, i would like to pose a general question here ( i didn't have an idea of any other suitable forum ). My protein active site has a GDP which is coordinated to a Mg ion. The Mg ion itself coordinates

Re: [gmx-users] Removing errors related to missing dihedrals.

in the dihedrals section of ffbonded.itp. How do we calculate these parameters for new dihedrals ? Thank you again With regards Abhishek On 2/12/13 6:19 AM, Abhishek Acharya wrote: Hello Justin. Help would really be appreciated. And yes you are correct and i thought the same. Initially I tried using

Re: [gmx-users] Removing errors related to missing dihedrals.

wildcard) imidazoles, indoles, purines I expected this to remove the errors 1, 2 and 3. I took care to keep the atomtypes order the same. But this doesn't seem to affect the result. I get the same errors. Any ideas?? Thank you again With regards Abhishek On 2/12/13 6:19 AM, Abhishek Acharya wrote

Re: [gmx-users] Removing errors related to missing dihedrals.

--- Thank you With Regards Abhishek Acharya Dear Gromacs Users. I generated a topology file of GDP for OPLSAA force field using MKTOP. But on running grompp I got a list of No default Angle types and No default Ryckaert Bell. types error

[gmx-users] Removing errors related to missing dihedrals.

-run. Is there anything wrong with this ? Do i need to edit some other related files. I am very new to gromacs. Kindly help as I'm stuck. Thanks in advance. Abhishek Acharya M.Tech Structural Biology Lab Biological Sciences and Bioengineering Department Indian Institute of Technology Kanpur. -- gmx