[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

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

From: Mark Abraham To: Discussion list for GROMACS users 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 in presence > of A

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

Discussion list for GROMACS users Sent: Tuesday, 23 June, 2009 11:16:26 AM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle wrote: > Hi, > >Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to pdb2gmx > and receive the error as "

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

problem or writing things in improper order ? Nikhil From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, 23 June, 2009 12:35:12 PM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle wrote: > Hi, >

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

? From: Justin A. Lemkul To: Discussion list for GROMACS users 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 energy of > the system w

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

? Regards, Nikhil From: Mark Abraham To: Discussion list for GROMACS users 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 file generated for EM sh

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

dynamics on my ATP-receptor complex system ? Regards, Nikhil From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, 23 June, 2009 12:35:12 PM Subject: Re: [gmx-users] simulation of protein in presence of ATP nikhil damle wrote: >

[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 http://lists.gro

[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___ gmx-use

Re: [gmx-users] query regarding g_rms

Thanks a lot for the help. Regards, Nikhil From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Monday, 13 July, 2009 5:22:06 PM Subject: Re: [gmx-users] query regarding g_rms nikhil damle wrote: > Hi, > What are the units of RMSD (nm

[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 fo

Re: [gmx-users] Hello

From: Mark Abraham To: Discussion list for GROMACS users 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. But > even after using nstcomm=1

Re: [gmx-users] Hello

uld have peptide displaced ? Regards, Nikhil From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, 14 July, 2009 12:28:05 PM Subject: Re: [gmx-users] Hello nikhil damle wrote: > I am turning pbc =xyz as written in earlier correspondence.

[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 individua

[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 http://li

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

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 o

Re: [gmx-users] H-Db error

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, it gives error of missing atom

Re: [gmx-users] H-Db error

3a1 --- From: Justin A. Lemkul To: Discussion list for GROMACS users 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 of a residue which is > t

Re: [gmx-users] H-Db error

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 msg ? i added thi

[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's breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/___

[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 http://cricket.yahoo.com___

Re: [gmx-users] Query regarding phosphothreonine parameters

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://o

[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 expe

[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 spike

Re: [gmx-users] Probelm of g_rms

Yes. I am correcting the trajectory for periodicity Regards, Nikhil From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Wednesday, 23 September, 2009 3:48:47 PM Subject: Re: [gmx-users] Probelm of g_rms nikhil damle wrote: > Hi

[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) dens

[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) den

[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, t

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

ance 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 charge). As

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

GROMACS users 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 twice the cut-off le

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

lowed cell size(2.00)" What possibly could be the reason ? Regards, Nikhil ____ From: nikhil damle To: Discussion list for GROMACS users Sent: Thu, 8 October, 2009 2:10:04 PM Subject: Re: [gmx-users] Load imbalance and Y size error No. My system is a sing

[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 cut-of

Re: [gmx-users] domain decomposition error

ikhil From: Justin A. Lemkul To: Discussion list for GROMACS users 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 with ATP and &g

[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] 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

Re: [gmx-users] Distance restraint energy terms

rms nikhil damle wrote: > 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 > princip

Re: [gmx-users] Distance restraint energy terms

equal for both pairs. Am I understanding correctly ? Regards, Nikhil From: nikhil damle To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Mon, 8 February, 2010 10:14:10 AM Subject: Re: [gmx-users] Distance restraint energy terms I have already

[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

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 solvate

[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 solvat

[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 g