[gmx-users] Making Disulfide Bonds

Dear Gromacs Users! I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage. Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also I've tried to check this bond in pymol and found that distance between

Re: [gmx-users] Making Disulfide Bonds

to recalculate the topology. Francesco 2012/4/28 James Starlight jmsstarli...@gmail.com Dear Gromacs Users! I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage. Unfortunatelly one of that S-S have not been recognised

Re: [gmx-users] Making Disulfide Bonds

). As the result I have not noticed any perturbation in the distance between two S-S atoms the distance between wich I've constrained. 2012/4/28 James Starlight jmsstarli...@gmail.com Hi Francesco! So I must define in the current topology the disres bettwen two S atoms ( in the below example

Re: [gmx-users] Making Disulfide Bonds

...@vt.edu On 4/28/12 10:08 AM, James Starlight wrote: .. and the main question- what should be in mdp file of such restrained minimisation ? Today I've done vry properly minimisation of such system in vacuum with the CG minimisator and applied disres ( above example ) with big force

Re: [gmx-users] Coordinate file for lipid bilayer

not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC

[gmx-users] Measure of density in homo- and heterogeneous systems

Dear Gromacs users! In this task I have two systems: First system consist of single layer of Ccl4 molecules. Second system consist of membrane-mimicking layer of Ccl4 surrounded by water and the protein embedded in that biphastic layer. I'd like to measure density in both of my systems to

Re: [gmx-users] Measure of density in homo- and heterogeneous systems

Justin, the main problem is the my simulation in nvt ensemble :) I understand that density is constant in that conditions but I'd like to find way to check this values for different components of my system. James 2012/5/28 Justin A. Lemkul jalem...@vt.edu On 5/28/12 3:09 PM, James

[gmx-users] parameters for bond types for GROMOS force field.

Dear Gromacs Users! I'm looking for description of the parameters of bonds terms ( termed as the gb_# in the topology.top file) . Could you tell me where I could find such descriptions for all possible bond types ? thanks, James -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] parameters for bond types for GROMOS force field.

; CH2 - C, CR1 (6-ring) 800 and for the second one ; #define gb_11 0.1340 1.0500e+07 ; C - N, NZ, NE 900 ? Thanks for help James 2012/6/8 Mark Abraham mark.abra...@anu.edu.au On 9/06/2012 12:00 AM, James Starlight wrote: Dear Gromacs Users! I'm looking

Re: [gmx-users] parameters for bond types for GROMOS force field.

ring system Thanks again, James 2012/6/8 Justin A. Lemkul jalem...@vt.edu On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C

Re: [gmx-users] parameters for bond types for GROMOS force field.

Justin, thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C) for parametrisation in my task. James 2012/6/8 Justin A. Lemkul jalem...@vt.edu On 6/8/12 2:01 PM, James Starlight wrote: Justin, Does the gb_10 suitable for both bonds that I want to parametrise

[gmx-users] Re: Automated Topology Builder job partially completed

Justin, I have also question about inclussion of the part of the topology file wich was done by the external server ( e.g by ATB) in the topology of my molecule. E.g I'm working with GFP wich include non-standart chromophore group wich is covalent bonded to the all protein. So I've extracted

Re: [gmx-users] parameters for bond types for GROMOS force field.

I would like to present as the rigid. I've change to the ga_27 ( 120) but during simulation the bond was still in sp3. What I've done wrong ? James 2012/6/8 James Starlight jmsstarli...@gmail.com Justin, thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C

Re: [gmx-users] parameters for bond types for GROMOS force field.

would not work properly :( James 2012/6/10 Justin A. Lemkul jalem...@vt.edu On 6/10/12 3:06 AM, James Starlight wrote: Justin I have one extra question about parametrisation of the bond type Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've changed bond type

Re: [gmx-users] parameters for bond types for GROMOS force field.

:( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as thega_27 but it also could not help me. James 2012/6/10 Justin A. Lemkul jalem...@vt.edu On 6/10/12 8:03 AM, James Starlight wrote: Justin, thanks

Re: [gmx-users] Coordinate file for lipid bilayer

the lines in each lipid, and use editconf -f file.gro -resnr 1 to renumber) the way it is written in the topology. Cheers Jon On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined

[gmx-users] analysing of the long trajectories

Dear Gromacs Users! I've forced with the problem during analysing of long trajectories consisted of 5000 calculated for average system ( ~ 35000 atoms). Commonly I use VMD for analysing of such task but in case of long trajectories loading this software has been crashed with the memory eror

Re: [gmx-users] analysing of the long trajectories

in the xtc format James 2012/6/12 Mark Abraham mark.abra...@anu.edu.au On 12/06/2012 4:20 PM, James Starlight wrote: Dear Gromacs Users! I've forced with the problem during analysing of long trajectories consisted of 5000 calculated for average system ( ~ 35000 atoms). Commonly I use VMD

[gmx-users] Insertion protein in the membrane via G_membed

Dear Gromacs Users! I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed. I've done all steps in accordance to the KALP tutorial ( I've oriented both membrane as well as the protein in the same dimensions merged both topologies and gro files in

Re: [gmx-users] Insertion protein in the membrane via G_membed

) but I've obtained exactly the same results. James 2012/6/14 Mark Abraham mark.abra...@anu.edu.au On 14/06/2012 4:39 PM, James Starlight wrote: Dear Gromacs Users! I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed. I've done all steps

Re: [gmx-users] analysing of the long trajectories

. Note that larger systems require more frames, as there will be more large scale dynamics to characterize. Cheers, Tsjerk On Tue, Jun 12, 2012 at 9:29 AM, James Starlight jmsstarli...@gmail.com wrote: Mark, Thanks for advise. As I've found in that link the main way to reduce

Re: [gmx-users] analysing of the long trajectories

By the way, I'm also looking for a most trivial way for extraction of pdb files from my trajectory on the desired intervals. E.g I have trajectory consisted of 5000 frames and I want to obtain 10 pdb files every each 500 frames ( or selected time interval as the alternative ). Commonly I do it

Re: [gmx-users] Insertion protein in the membrane via G_membed

-range interactions I've used from my typical simulation on the lipid Gromos56-ff ( presented in the Justin's tutorial). Is there any other parameters for that object wich are most suitable for G_membed ? James 2012/6/14 James Starlight jmsstarli...@gmail.com Mark, I've used commands

[gmx-users] Expanding existing biphastic Box

Dear Gromacs Users! I have biphastic system wich consist of Ccl4 layer between 2 layers of water with the dimensions 8 6 10. I want to expand this box on Y dimension from 6 to 8 nm in both ccl4 and water layers. Is there any trivial ways to do add new Ccl4 and solvent molecules to the existing

[gmx-users] Analysis of the torsion Chi angles dynamics during simulation

Dear Gromacs Users! I want to perform analysis of the chosen Chi1 angles during md simulation. How I could obtain such graphs with the dependence of the dynamics ( distribution in degrees) of that torsions on the simulation time ? Thanks for help James -- gmx-users mailing list

Re: [gmx-users] Insertion protein in the membrane via G_membed

-Field-zero The parameters for long-range and short-range interactions I've used from my typical simulation on the lipid Gromos56-ff ( presented in the Justin's tutorial). Is there any other parameters for that object wich are most suitable for G_membed ? James 2012/6/14 James Starlight

Re: [gmx-users] Insertion protein in the membrane via G_membed

index.ndx and didt not find POP group in my first Protein_ADN group. Why this error should be ? 2012/6/20 Mark Abraham mark.abra...@anu.edu.au On 20/06/2012 4:39 PM, James Starlight wrote: by the way I've forced with problems during insertion of the complex protein_ligand into membrane

Re: [gmx-users] Insertion protein in the membrane via G_membed

2012/6/20 Mark Abraham mark.abra...@anu.edu.au On 20/06/2012 5:08 PM, James Starlight wrote: Mark, I've made changes in the input mdp file integrator = md energygrps = Protein_ADN freezegrps = Protein_ADN freezedim = Y Y Y energygrp_table energygrp_excl

[gmx-users] Analysis of buried water dynamics

Dear Gromacs users! I'm simulatting membrane receptor in the explicit membrane surrounded by water. Durring this MD run I've noticed that individual waters move into the receptor interiour from the surroundings leaflets ( In my case mainly from upper leaflet). How I could examine dynamics of

[gmx-users] Crashes during protein-ligand simulation

Dear Gromacs users! I have some problems with the simulation of protein-ligand complex embedded in the ccl4-water environment. In addition there are some crystallography waters (xw) embedded in the protein interiour of the protein. I've done equilibration and minimisation of my system and run it

Re: [gmx-users] Crashes during protein-ligand simulation

if the problem was with that COM motion James 2012/7/6, Justin A. Lemkul jalem...@vt.edu: On 7/6/12 1:12 AM, James Starlight wrote: Dear Gromacs users! I have some problems with the simulation of protein-ligand complex embedded in the ccl4-water environment. In addition there are some

Re: [gmx-users] Crashes during protein-ligand simulation

:05 PM, James Starlight wrote: Justin, I've done all steps in accordance to your tutorial. I've already done the same systems with another ligands but had no problem. This time I've made topology of the ligand via ATB server. I've only noticed that some cgnr are too big in that topology

Re: [gmx-users] Crashes during protein-ligand simulation

I do based on that values ? How I could measure stability of the ligand ( beside dirrect RMSD measurement) from such energy terms? James 2012/7/6, Justin A. Lemkul jalem...@vt.edu: On 7/6/12 3:56 PM, James Starlight wrote: Justin, I've experimented with 2 dirrerent COM groups comm-grps

Re: [gmx-users] Crashes during protein-ligand simulation

could be ? James 2012/7/7, Justin A. Lemkul jalem...@vt.edu: On 7/7/12 11:08 AM, James Starlight wrote: justin, It seems that problem was in the big charge groups in the ligand.itp file. In particularly I've devided largest group into several smaller and there haven't any crashes been occured

[gmx-users] Simulation under collision thermostat

Dear Gromacs Users! I want to perform my simulation under conditions with collisional thermostat (where each atom is bombarded by virtual particles with Maxwell speed distribution) instead of thermostat with alternate friction ( like Nose Hoover which I'm using after my system have been

[gmx-users] Re: Simulation under collision thermostat

Dear all! I've still could not find any possibilities of ussage of collision thermostat :( But as I've noticed I can use SD integrator which could mimic such conditions. As I've understood the usage of that integrator exclude t_couple option from mdp file. If I'd like to use SD as the

[gmx-users] Merging of two trajectories

Dear Gromacs Users! I have two trajectories with removed PBC which was done by the below command. trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc mol -ur compact Both of that trajectories are of the same system- when one trajectory have been manyally stoped I've run the

Re: [gmx-users] Merging of two trajectories

this occurs ? By the way if I'm using -cat option resulted file consist of both trajectories ( in the separate enties). James 2012/7/18 Justin Lemkul jalem...@vt.edu: On 7/18/12 7:35 AM, James Starlight wrote: Dear Gromacs Users! I have two trajectories with removed PBC which was done

Re: [gmx-users] Merging of two trajectories

Justin thanks, Works perfect. James 2012/7/18 Justin Lemkul jalem...@vt.edu: On 7/18/12 9:34 AM, James Starlight wrote: Justin thanks for advise I've used the bellow command for both trajectory trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc but resulted

[gmx-users] Simulation of the protein-ligand system embedded in membrane

Dear Gromac's users! I have some questions about simulation of the membrane protein complexed with it's ligand in the membrane environment. 1- I want to simulate number of such similar systems ( e.g protein in POPC bilayer) which differs only in ligand complexed into protein interiour. Should I

Re: [gmx-users] Simulation of the protein-ligand system embedded in membrane

Mark, Only if the apo form has room for you to cut and paste in all your ligands... You'll have to equilibrate independently in each case, so you don't gain anything by not creating the system from the beginning each time. This can gain in terms of avoiding of time-consumptions solvation

[gmx-users] molecular composition of the system

Dear Gromacs users! Sometimes I need to calculate exact numbers of different molecules of my system based on the initial gro file to add this information at the end of the topol.top file. Its not trivial task for the big heterogeneous systems ( e.g protein embeded into the membrane solvated in

[gmx-users] Analysis of protein-ligand interactions

Dear Gromacs Users! I want to analyze protein-ligand polar interactions by means of g_hbond utility In particular I want to obtain some map wich include information aabout dynamics of the h bonds occurence between defined polar groups of the protein ( active site) and ligand polar atoms. For

[gmx-users] Preparation of the pdb for MD simulation

Dear Gromacs users! I have pdb structure wich I'd like to prepare for my MD simulation. In that case this structure consist of some non-standart residue ( chromophore) wich is covalently bonded to the protein's backbone. The main problem is that this structure has some missing residues on both

[gmx-users] Adding New Residue to the Gromos 53.6 ff

Dear Gromac's users! I'm working with the GFP protein which has chromophore (CRO) group which is covalently bonded to the protein. I want to add new residue to the Gromos 53.6 ff. by means of algorithm described here. For that I've coppied files to my local work dirr and modify all of them in

Re: [gmx-users] Re: Adding New Residue to the Gromos 53.6 ff

is covalently linked in the midle of the alph helix of that protein in both ends) James 2012/8/5, Mark Abraham mark.abra...@anu.edu.au: James Starlight wrote Dear Gromac's users! I'm working with the GFP protein which has chromophore (CRO) group which is covalently bonded to the protein. I want

Re: [gmx-users] Re: Adding New Residue to the Gromos 53.6 ff

be some script foe convertion itp ro rtp because both of that formats have a lot of differenties so the manually editing in case of big HET group is very routinely. James 2012/8/5, Mark Abraham mark.abra...@anu.edu.au: On 6/08/2012 4:31 AM, James Starlight wrote: Mark, 1) The error was because

Re: [gmx-users] Re: Adding New Residue to the Gromos 53.6 ff

cases more usefull that ITP. James 2012/8/5, Mark Abraham mark.abra...@anu.edu.au: On 6/08/2012 4:11 PM, James Starlight wrote: Mark, I suppose that the most trivial way to include such external topologies is the placement of the ITP file at the bottom of the topol.top file ( and addition

[gmx-users] Cross-correlation maps

Dear Gromacs users! I want to obtain Cross-correlation maps ( for indication of the cross-correlated fluctuations of the residues). The example of such maps can be found here http://pubs.acs.org/doi/abs/10.1021/ja076046a I found that modificied version of the G_covar from users contributions

[gmx-users] Re: Cross-correlation maps

( e.g fluctuations in case of apo form were more frequent than in case of liganded form). IS there any way to direct mesure and comprison of such side-chain's dynamics for two trajectories? James 2012/8/15, James Starlight jmsstarli...@gmail.com: Dear Gromacs users! I want to obtain Cross

Re: [gmx-users] Re: Cross-correlation maps

filtered.xtc from the first 50 principal components. How I should analyse possible cross-correlations of the fluctuations of the side-chains? James 2012/8/27 Mark Abraham mark.abra...@anu.edu.au: On 24/08/2012 4:51 PM, James Starlight wrote: up :) It's appeared two additional questions. 1

Re: [gmx-users] Re: Cross-correlation maps

of information, which you could solve with correlations? Cheers, Tsjerk On Aug 27, 2012 4:01 PM, James Starlight jmsstarli...@gmail.com wrote: Mark, Is there any way to calculate such cross-correlations without calculation of the covariance matrix ( from the MD trajectory indirectly) ? I've noticed

Re: [gmx-users] Re: Cross-correlation maps

Mark, Thanks for explanation! 2012/8/27, Mark Abraham mark.abra...@anu.edu.au: Did you construct a correlation matrix from side chain atoms? Yes, and there is some degree of correlation between adjacent side chains but lack of any cooperativety between distant side-chains. In comparison in

[gmx-users] Different initial conditions for the membrane protein simulation

Dear Gromacs Users! I'm simulating intrinsic dynamics of some membrane receptors which can have functional relevance. Therefore I'm looking for the most suitable initial conditions of my simulation which could provide maximal degree of such dynamics (arisen from the cooperative thermal

[gmx-users] On the usage of the Noose-Hover chains

Dear Gromacs Users! From gromacs manual I've found that the usage of Noose-Hover chains require not a leap-frog integrator ( e.g md-vv as the alternative) as well as specil definition of the number of chains which must be defined in the special environment variable GMX_NOSEHOOVER_- CHAINS could

Re: [gmx-users] Different initial conditions for the membrane protein simulation

of that conformers onto some principal components? James 2012/9/10, Mark Abraham mark.abra...@anu.edu.au: On 11/09/2012 2:36 AM, James Starlight wrote: Dear Gromacs Users! I'm simulating intrinsic dynamics of some membrane receptors which can have functional relevance. Therefore I'm looking

[gmx-users] Resuming of calculation from last *.cpt

Dear Gromacs Users! I'm looking for possible way to resume trajectory calculations after that calculations have been stoped. Typically in such cases I start new task using cpt file from incomplete run. This produce new trajectory which start from the last frame of previous run. After that I

Re: [gmx-users] Resuming of calculation from last *.cpt

to the name of old trajectory ) that produce new .trr .edr and other files and back up old ( e.g crete #incomplete.trr etc) ones instead of continuation of the existing ( incomplete ) trajectory What I've done wrong? 2012/9/13, Justin Lemkul jalem...@vt.edu: On 9/13/12 1:12 AM, James

Re: [gmx-users] Resuming of calculation from last *.cpt

(md_initial) without creation of new ones ? James 2012/9/13 Justin Lemkul jalem...@vt.edu: On 9/13/12 9:56 AM, James Starlight wrote: Justin, I've used grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o incomplete.tpr mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete

Re: [gmx-users] Resuming of calculation from last *.cpt

trajectory and other files. James 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where

Re: [gmx-users] Resuming of calculation from last *.cpt

In that case I've obtain error Fatal error: Failed to lock: md_init.log. Already running simulation? What does it means ? the md_init.log is present in the wor dir 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:11 AM, James Starlight wrote: Jusin, yes, the initial files were

[gmx-users] Analysis of enssemble of MD trajectories

Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as

Re: [gmx-users] Analysis of enssemble of MD trajectories

out by the later Vs 0.4 and 5% meaning no change) Hope that helps, and if I am wrong about something somone corrects me. Stephan Watkins Original-Nachricht Datum: Thu, 20 Sep 2012 14:06:40 +0400 Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS

Re: [gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins

this values would be correct in 54A7 ff as well ? What addition parameters of that ff should I take into account during simulation of my protein-lipid system ? ( I'm simulate in npt ensemble with SD integrator withot t_coupl ) James 2012/9/21, Justin Lemkul jalem...@vt.edu: On 9/21/12 2:33 PM, James

Re: [gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins

( protein+lipids+water). So I have protein and spc water parametrised in 54a7 ff and lipids - in berger's 53a6. If new 54a7 ff include only updates to dihedrals should I use old cut-offs ? James 2012/9/22, James Starlight jmsstarli...@gmail.com: Justin, I've integrated berger's lipid

Re: [gmx-users] pca-based MD

Sampling on these PCs to explore the conformational space that is highly correlated to the volume of the active site. After that, one could safely claim that the Hypothesis was true or false. I would be interested to read your comments on this. Thomas On 23 September 2012 11:19, James Starlight

Re: [gmx-users] pca-based MD

as MD_data) James 2012/9/23 Thomas Evangelidis teva...@gmail.com: On 23 September 2012 17:18, James Starlight jmsstarli...@gmail.com wrote: Thomas, thank you for the explanation 1) Indeed ED sampling was exactly that I need. It's not quite understand for me about correct chose

Re: [gmx-users] Analysis of enssemble of MD trajectories

Justin, Francesco, thanks for advises. James 2012/9/21 Justin Lemkul jalem...@vt.edu: On 9/21/12 2:11 AM, James Starlight wrote: Dear collegues Thank for advices. Indeed Gromacs is able to analyse two trajectories with g_rms ( with the flags -f and -f2 ) but as the result I've obtain

Re: [gmx-users] pca-based MD

I've tried to make PCA from my X-ray data and forced with many problems :) Firstly I've made pdb trajectory in NMR-like format ( by means of pymol) consisted of all X-ray structures. than I've make .tpr file (From the tpr of the same protein which I've simulated previously) for the subset of

Re: [gmx-users] pca-based MD

-deffnm MD -ei sam.edi I obtain error about mismatching of atom number from the edi as well as system.tpr . Is there any way to extrapolate number of atoms in the sam.edi ? James 2012/9/23, James Starlight jmsstarli...@gmail.com: I've tried to make PCA from my X-ray data and forced with many

Re: [gmx-users] pca-based MD

(althought I've extracted eigenvectors from c-alpha only) and 46185- full system includding membrane and SOL in that case. Does it mean that such method is only applicable for biassed simulations of the systems in vacuu or with implicit solvent ? James 2012/9/24 James Starlight jmsstarli...@gmail.com

[gmx-users] Assignment of new velocities for multi-runs

Dear All! I'd like to perform several simulations of the membrane protein started from the common conditions which differs only in the initial velocities ( for each simulation random speed distribution will be used from the Maxwell distribution). Because I simulate membrane protein the long

Re: [gmx-users] Assignment of new velocities for multi-runs

at NVT with different values of gen_seed). -Justin On 2012-09-28 11:59:02PM -0700, James Starlight wrote: Dear All! I'd like to perform several simulations of the membrane protein started from the common conditions which differs only in the initial velocities ( for each simulation random speed

Re: [gmx-users] Coordinate file for lipid bilayer

layers but the lipid number was the same. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Thanks for help, James 2012/6/11, Justin A. Lemkul jalem...@vt.edu: On 6/11/12 6:05 AM, James Starlight wrote: Dear

Re: [gmx-users] Coordinate file for lipid bilayer

of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 2:16 PM, James Starlight wrote: Dear all

Re: [gmx-users] Coordinate file for lipid bilayer

and y is thinker than water ( so the lipid number stay the same after resizing). James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 2:56 PM, James Starlight wrote: Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids

Re: [gmx-users] Coordinate file for lipid bilayer

:49 PM, James Starlight wrote: Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower

Re: [gmx-users] Coordinate file for lipid bilayer

with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 4:12 PM, James Starlight wrote

Re: [gmx-users] Coordinate file for lipid bilayer

are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 1:59 AM, James Starlight wrote: Justin, I've told about lower lipid density at the left and right edges of the new system

Re: [gmx-users] Coordinate file for lipid bilayer

:59 AM, James Starlight wrote: Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all

Re: [gmx-users] Coordinate file for lipid bilayer

Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I

Re: [gmx-users] Coordinate file for lipid bilayer

:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin

[gmx-users] problem with the index.ndx for EDS simulation

Dear Gromacs Users! I'd like to perform Essential Dynamics Sampling simulation in the Contraction mode targeted to the active.pdb structure of my protein. That X-ray structure lacks some atoms in comparison to the structure of that proteins which I've used in My md run from which eigenvectors for

Re: [gmx-users] Energy estimations of the protein-ligand complexes

? Mark On Mon, Dec 3, 2012 at 6:54 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I'm simulating different complexes of the receptors with different ligands. For each complex I want to determine potential energy (not the binding energy) of the ligand molecule

[gmx-users] Green fluorescent protein's chromophore

Dear Gromacs Users! I'm looking for the model as well as for the pre-paired topology for any kind of GFP protein with the chromophore group covaletnly bonded in the interiour of that protein. Some times ago I've tried to make such models by hands but I've forced with some difficulties with the

Re: [gmx-users] Green fluorescent protein's chromophore

. --- BHARAT On Wed, Dec 5, 2012 at 10:14 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs Users! I'm looking for the model as well as for the pre-paired topology for any kind of GFP protein with the chromophore group covaletnly bonded in the interiour of that protein. Some

Re: [gmx-users] Green fluorescent protein's chromophore

of different types of that chromophores so manual conversion of the ITP to RTP formats in each cases ( I'd like to simulate different mutants) would be very routinely. James 2012/12/5 Justin Lemkul jalem...@vt.edu: On 12/5/12 11:00 AM, James Starlight wrote: Hi Bharat, That simulation have been

Re: [gmx-users] Green fluorescent protein's chromophore

? Thanks for help James 2012/12/5 Justin Lemkul jalem...@vt.edu: On 12/5/12 11:19 AM, James Starlight wrote: Justin, The GFP protein consist of chromophore group which matured after folding of that protein. That prostetic group is the cyclized derivative of the Ser-Tyr-Gly peptide which

Re: [gmx-users] Green fluorescent protein's chromophore

Justin, thanks again for explanation. I'll try find other possible more automatic ways for conversion of the itp to rtps. If I've success I'll post here :) James tin Lemkul jalem...@vt.edu: On 12/5/12 11:46 AM, James Starlight wrote: Justin, So as I understood such problems might

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

for instance. By the way is there any suitable builing blocks (implemented in the rtp enties of the gromos ff) which could be used for charge assignment? James 2012/12/5 Justin Lemkul jalem...@vt.edu: On 12/5/12 12:57 PM, James Starlight wrote: Dear Gromacs Users! In one of my study I

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

13.0190 ; -0.000 27 CH11_N4HC2*70.200 13.0190 28OA1_N4HO2*7 -0.614 15.9994 29 H1_N4HH8M70.414 1.0080 ; 0.000 James 2012/12/5 Justin Lemkul jalem...@vt.edu: On 12/5/12 1:39 PM, James Starlight wrote

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

by another algorithm implemented in ATB ( am1 instead of pm3 which was used in the crashed simulation). James 2012/12/6, Justin Lemkul jalem...@vt.edu: On 12/6/12 2:39 AM, James Starlight wrote: Justin, Could you provide me with the example of the server where I could obtain Gromac's itp

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

. It's intresting that with the prodrg topology of that mollecule ( with worst charge distribution) I've never such problems. Might that error be due to the wrong geometry parametrisation (e.g incorect dihedrals) of the cGMP made by ATB ? James 2012/12/6 James Starlight jmsstarli...@gmail.com

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

representation :) James 2012/12/7 Justin Lemkul jalem...@vt.edu: On 12/7/12 10:41 AM, James Starlight wrote: Today I've tried to simulate complexes of my protein with the cyclic GMP parametrized by ATB's. (below the recent parametrisation for charges of that molecule done by am1 algorithm

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

anybody know another servers for parametrization of the ligands for charmm simulation in gromacs? 2012/12/7, Justin Lemkul jalem...@vt.edu: On 12/7/12 11:42 AM, James Starlight wrote: Justin, ligand-only simulation in vacuum have been finished with the same errors :) Step 19200, time 38.4 (ps

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

: On 12/7/12 11:42 AM, James Starlight wrote: Justin, ligand-only simulation in vacuum have been finished with the same errors :) Step 19200, time 38.4 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025443, max 0.140660 (between atoms 1 and 3) bonds that rotated more

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

] ? :) 4- Have anybody else used Swiss param for modeling protein-ligands systems? Might it be used with the charmm36 set ? James 2012/12/7, Justin Lemkul jalem...@vt.edu: On 12/7/12 2:21 PM, James Starlight wrote: Justin, with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw

[gmx-users] Analysis of solvent dynamics

Dear Gromacs Users! I want to study dynamics of solvent burried into the protein interiour during simulation (to check solvent accessible area of different amino acid of my protein). Eg while simulating of Green Fluorescent protein I'd like to check how much water burried into the beta-can

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

. Lai p...@uab.edu: On 2012-12-08 03:20:54AM -0800, James Starlight wrote: 1- on what assumptions that blocks were generated ? This appears to be a swissparm-specific question. I don't know what algorithms it uses to match what are essentially pharmacophores in the new molecule with the common

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

-terminal? (I've delited both hydrogens from RTP as well as from HDB files but the problem didn’t resolved. Also I'm using -ignh on the input pdb to ignore all hydrogens from the model) James 2012/12/11, Justin Lemkul jalem...@vt.edu: On 12/11/12 6:04 AM, James Starlight wrote: Peter, thanks

  1   2   3   4   5   >