[gmx-users] Please help

, With reagards Anik Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing

[gmx-users] DNA MD PROBLEM

Hello, This is Anik Sen from India. Am using Gromacs 4.5.5. to do some calculations on solvation and ligand binding interactions with DNA. I have some questions regarding the problem. As water is present in the system, so according to the manual the define in the .mdp file must be

RE: [gmx-users] to know about constraints

Dear Mark, i GOT IT. I understood my mistake and now it is running. Thanx for your help. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Wednesday, June 20, 2012 2:50 PM To: Discussion

RE: [gmx-users] to know about constraints

rg] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Wednesday, June 20, 2012 1:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 20/06/2012 5:24 PM, Anik Sen wrote: > Hello Justin > > For freezefprs, am using the .mdp file as follows:

RE: [gmx-users] to know about constraints

-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, June 20, 2012 12:09 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] to know about constraints On 6/19/12 2:35 PM, Anik Sen wrote: > Hello Justin, > This is Anik agai

RE: [gmx-users] to know about constraints

, which i donot want. Please help in this matter. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Anik Sen [anik...@csmcri.org] Sent: Tuesday, June 19, 2012 11:13 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: RE: [gmx-users] to

RE: [gmx-users] to know about constraints

] to know about constraints On 6/19/12 1:28 PM, Anik Sen wrote: > Dear gromacs developers, > > This is Anik. For a certain work with > nonbonded interactions with alkali halides and water, I need to constrain some > specific atoms in the energy mi

[gmx-users] to know about constraints

calculation. The water molecules and other atoms may be in movement during the calculation. Thanx in advance Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri

[gmx-users] hello

with the water molecules may not hamper but it may not dance so much in the solvation box. Thanx in advance Anik Sen. Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 36

RE: [gmx-users] Regarding errors

Dear Suryanarayana Seera Please check the itp files mentioned in the topol.top and what u used in your commands. Especially check the solvent model. May be you have not changed that in the topol.top file. From: gmx-users-boun...@gromacs.org [gmx-users-boun...

[gmx-users] problem

Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. I was trying to run the dynamics for some inorganic metal halides solvation in water. A fatal error is comingthat: * Atomtype "CH2r" not found. But in my system I have no such atoms. Only water molecules with t

[gmx-users] Cut off problem

ve already changed the ‘d’ and ‘rlist’; rvdw’ and rcoulomb’ to a number of different values to overcome the problem, but the problem persists. How can I overcome this problem. Thanking you in advance Anik Sen ======== Anik Sen Student CSIR-Ce

[gmx-users] To know

Hi, Am Anik Sen, using gromacs 3.3.2 version. I have a very simple question to ask, In the mdp file, like the emmod.mdp or run.mdp needed for a MD run there are three factors namely, rlist, rcoulomb and rvdw. 1. Is there any minimum value for these three below which the results will be

[gmx-users] (no subject)

number. 2. I have three different substrates. I want to create a same box size irrespective of the size of my molecule and generate same number of water molecules around them. What should I do? Thanking in advance. Anik Anik Sen

RE: [gmx-users] A query

___ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, January 31, 2012 7:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] A query On 31/01/2012 9:04 PM, Anik Sen wrote: Hello,

[gmx-users] A query

e topology database, but an atom of that name was not found in residue number 31. Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org]

[gmx-users] A query

ram pdb2gmx, VERSION 4.5.5 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OH in residue DG5 1 was not found in rtp entry DG5 with 31 atoms while sorting atoms. Thanks in advance Anik Sen Student CSIR-Central Salt & Mar

[gmx-users] (no subject)

residue DG5 1 was not found in rtp entry DG5 with 31 atoms while sorting atoms. Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] --

[gmx-users] topology missing

e. Whats the reason? Thanking n advance Anik ======== Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] ==

RE: [gmx-users] a query

...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, January 24, 2012 3:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] a query On 24/01/2012 8:32 PM, Anik Sen wrote: Hello Anik here. I think its a silly question but, could not stop to ask as its between

[gmx-users] a query

ed mol. So what will be the residue files for DNA. Please suggest. Thanks in advance. ======== Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [

RE: [gmx-users] (no subject)

did you exactly installed fftw and gromacs in order to get more help. It seems to me that the problem is related to the shared fftw libraries. Could you compile the gromacs binaries with --disable-shared? Javier El 11/01/12 12:07, Anik Sen escribió: I have already done that but the problem persi

RE: [gmx-users] (no subject)

subject) Hi You should compile your fftw with --enable-shared if you want to link your gromacs installation to shared libraries (which is the default in the latest versions). Check the installation instructions in the website. Javier El 11/01/12 08:20, Anik Sen escribió: Im having problems

[gmx-users] (no subject)

1 Thanx in advance Anik ======== Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-users mailing

RE: [gmx-users] HEME topology

Dear nirmal, try prodrg server for generating the topology file for the said pdb file. Here is the link. http://davapc1.bioch.dundee.ac.uk/prodrg/ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Nirmal Prasad

[gmx-users] thanx

thanx justin for the help Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] -- gmx-u

[gmx-users] problem

' make: *** [all-recursive] Error 1 What to do? ==== Anik Sen Student CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg. Bhavnagar, Gujarat 364002 [www.csmcri.org] ==