[gmx-users] Energy minimisation query

Hi, I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly same parameters which i use for monomer during dimer minimisation in solvent. System Details: # Atoms = 4488 (# Res = 582) octahedron box with d = 0.9 Solvent (spce water model)

[gmx-users] Energy minimization query

Hi, I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly same parameters which i use for monomer during dimer minimisation in solvent. System Details: # Atoms = 4488 (# Res = 582) octahedron box with d = 0.9 Solvent (spce water model)

[gmx-users] position restraint....NEED URGENT HELP

Hey ! My doubt posted few days back still holds. I am trying to simulate the kinase domain in complex with cyclin. when i keep entire complex either position restrained or flexible, MD runs without any errors. But as soon as i keep cyclin position restrained keeping kinase domain flexible, it

[gmx-users] Position restrained Dynamics

Hi All, I am trying to simulate kinase domain (chain A) in complex with cyclin (chain B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need to keep only kinase domain flexible but cyclin fixed. i put POSRES_B in define variable and tried to simulated the entire

Re: [gmx-users] Regarding genconf

Hi Vinod, How did you build your top file for input to grompp ? genconf would have given you a multiplied system in .gro structure format. I think you should generate .top file from this .gro file using pdb2gmx and then use that as grompp input. Regards, Nikhil

[gmx-users] Position restrained Dynamics

Hi All, I am trying to simulate kinase domain (chain A) in complex with cyclin (chain B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need to keep only kinase domain flexible but cyclin fixed. i put POSRES_B in define variable and tried to simulated the entire

Re: [gmx-users] Distance restraint energy terms

be equal for both pairs. Am I understanding correctly ? Regards, Nikhil From: nikhil damle pdnik...@yahoo.co.in To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, 8 February, 2010 10:14:10 AM Subject: Re: [gmx-users] Distance

[gmx-users] Distance restraint energy terms

Hi, I have applied distance restraints on my system during MD simulation through following options: disre = simple and disre_fc = 2000 in .mdp file. Now i wish to see the energy term corresponding to these restraints in principle to be written in .edr file. But g_energy programme does not list

[gmx-users] Vacuum FF in Gromacs-4.0.5

Hi, I wanted to inquire about the vacuum FF distributed officially with GROMACS-4.0.5. I wish to carry out a vacuum MD of ~300 aa protein FF.dat file mentions of G43b1 as officially distributed vacuum FF. But there are no FF related files-.rtp,.hdb etc present. Is that the case that GROMACS-4

[gmx-users] domain decomposition error

Hi, I am trying to run a vacuum simulation of a system associated with ATP and peptide. Being vacuum MD i removed pressure coupling and included plain electrostatic cut-offs while calculating potential. Energy minimisation converged to machine precesion even though not upto the specified

Re: [gmx-users] domain decomposition error

From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sun, 11 October, 2009 4:20:58 PM Subject: Re: [gmx-users] domain decomposition error nikhil damle wrote: Hi, I am trying to run a vacuum simulation of a system associated

[gmx-users] Load imbalance and Y size error

Hi all I am trying to simulate a system of 3168 atoms in vacuum in PBC box (-d=0.9 nm). Since there are no solvent molecules, i am unable to neutralise the system using addition of ions (Hence system has +3 charge). As soon as i start the MD run after putting the whole system in box,

Re: [gmx-users] Load imbalance and Y size error

Subject: Re: [gmx-users] Load imbalance and Y size error nikhil damle wrote: Hi all I am trying to simulate a system of 3168 atoms in vacuum in PBC box (-d=0.9 nm). Since there are no solvent molecules, i am unable to neutralise the system using addition of ions (Hence system has +3

Re: [gmx-users] Load imbalance and Y size error

To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, 8 October, 2009 12:46:56 PM Subject: Re: [gmx-users] Load imbalance and Y size error nikhil damle wrote: Hi, I tried to run on single node now. Now the error is different saying One of the box vectors has become shorter than

Re: [gmx-users] Load imbalance and Y size error

size(2.00) What possibly could be the reason ? Regards, Nikhil From: nikhil damle pdnik...@yahoo.co.in To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, 8 October, 2009 2:10:04 PM Subject: Re: [gmx-users] Load imbalance and Y size

[gmx-users] Regarding g_rms

Hi, I am simulating a protein system and willing to compute rmsd over entire trajectory wrt a starting crystal structure. i use g_rms programme for this purpose starting from 0th frame until last frame of time. But rmsd shows abnormal spikes between successive time-frames. Height of

[gmx-users] Probelm of g_rms

Hi all, I am facing the problem while calculating backbone RMSD over 30 ns. upto ~6-7 ns g_rms gives correct RMSDs and later all RMSD values are unexpectedly and unusually high (within 20 ps RMSD value shoots up by ~8A). But when i calculate RMSD using g_confrms programme, it gives me

[gmx-users] Query regarding Phosphate parameters

Hello, Where will I get Phosphothreonine parameters ? I have tried to incorporate gamma-Phosphate parameters from ATP in the threonine residue but in vain. regards, Nikhil See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz.

[gmx-users] Query regarding phosphothreonine parameters

Hello, Where will I get Phosphothreonine parameters ? I have tried to incorporate gamma-Phosphate parameters from ATP in the threonine residue but in vain. regards, Nikhil Love Cricket? Check out live scores, photos, video highlights and more. Click here

Re: [gmx-users] Query regarding phosphothreonine parameters

-users] Query regarding phosphothreonine parameters nikhil damle wrote: Hello, Where will I get Phosphothreonine parameters ? I have tried to incorporate gamma-Phosphate parameters from ATP in the threonine residue but in vain. The answer for parameterization is always the same: http

Re: [gmx-users] H-Db error

Sent: Monday, 20 July, 2009 7:35:29 AM Subject: Re: [gmx-users] H-Db error nikhil damle wrote: This is how i have modified the entry as i myself created the parameter file for phosphothreonine. This is normal NH hydrogen n no extra added=directly copied from threonine. So y there is an error

Re: [gmx-users] parameters for Phosphorylated threonine and serine

] parameters for Phosphorylated threonine and serine nikhil damle wrote: Hi, Can anyone suggest me where to get phosphorylated ser and threonine parameters ? The ffG43a1p tarball is available under User Contributions on the Gromacs website: http://www.gromacs.org/index.php?title=Download_

[gmx-users] H-Db error

Hi, I added peptide H to the the new residue i added to .rtp file in the ffG43a1.hdb file But the pdb2gmx gives error saying it can not read hdb file. If i remove this H from .hdb file, it gives error of missing atom. How should i resolve this problem ? y can pdb2gmx not read hdb file if i add

Re: [gmx-users] H-Db error

@gromacs.org Sent: Sunday, 19 July, 2009 2:43:05 PM Subject: Re: [gmx-users] H-Db error nikhil damle wrote: Hi, I added peptide H to the the new residue i added to .rtp file in the ffG43a1.hdb file But the pdb2gmx gives error saying it can not read hdb file. If i remove this H from .hdb file

Re: [gmx-users] H-Db error

--- From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 19 July, 2009 5:14:35 PM Subject: Re: [gmx-users] H-Db error nikhil damle wrote: Hello, Thanks for the reply. I am trying to add N-H hydrogen

[gmx-users] parameters for Phosphorylated threonine and serine

Hi, Can anyone suggest me where to get phosphorylated ser and threonine parameters ? Regards, Nikhil Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Protein going out of the box

Hello, When I am running energy minimisation of protein-peptide complex, minimised structure shows a space for the protein in water box; but peptide remains inside the box while protein is seen outside. Same occurs when I keep pbc = xyz and/or nstcomm = 1 in .top file, I am including

[gmx-users] Hello

I am carrying out energy minimization of the protein peptide complex. But even after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide far away from the binding site. This did not happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar .mdp file is given

Re: [gmx-users] Hello

From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 14 July, 2009 12:07:24 PM Subject: Re: [gmx-users] Hello nikhil damle wrote: I am carrying out energy minimization of the protein peptide complex

Re: [gmx-users] Hello

have peptide displaced ? Regards, Nikhil From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 14 July, 2009 12:28:05 PM Subject: Re: [gmx-users] Hello nikhil damle wrote: I am turning pbc =xyz

[gmx-users] query regarding g_rms

Hi, What are the units of RMSD (nm or ang) in which g_rms calculates the RMSD between two structures ? Regards, Nikhl Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php___

Re: [gmx-users] query regarding g_rms

Thanks a lot for the help. Regards, Nikhil From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 13 July, 2009 5:22:06 PM Subject: Re: [gmx-users] query regarding g_rms nikhil damle wrote: Hi

[gmx-users] (no subject)

Hi all, Thanks a lot for the help extended to me through gmx-users' archives. Regards, Nikhil Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] simulation of protein in presence of ATP

in presence of ATP nikhil damle wrote: Hi, We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the error is atom N not found in residue 1ATP while combining tdb and rtp pdb2gmx tries to cap termini of peptides

Re: [gmx-users] simulation of protein in presence of ATP

From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 23 June, 2009 9:10:15 PM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle wrote: OK till here done ! the pdb

Re: [gmx-users] simulation of protein in presence of ATP

or writing things in improper order ? Nikhil From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 23 June, 2009 12:35:12 PM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle

Re: [gmx-users] simulation of protein in presence of ATP

this ? From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 23 June, 2009 4:41:22 PM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle wrote: Thanks a lot for kind help. I reached till grompp before minimizing

Re: [gmx-users] simulation of protein in presence of ATP

Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 22 June, 2009 10:27:24 AM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle wrote: Hi all, I want to carry out a MD simulation of a receptor protein

[gmx-users] simulation of protein in presence of ATP

Hi all, I want to carry out a MD simulation of a receptor protein in presence of ATP molecule. ATP is included in .rtp file of ffG43a1 force field. but post pdb2gmx, .pdb output file does not show crds of ATP. Does it mean that ATP is not recognized as a residue of protein in spite of

[gmx-users] error... plz help

Dear all , I am trying to run energy minimisation of a modified PDB file (part of ATOM block copy-pasted in dummy.pdb file) it has number of missing atoms (in the original pdb file itself) . hence the .top file is created with option -missing. as it has charge of -2, i have added 2 Na+ ions