Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

for target `src/gmxlib/CMakeFiles/gmx.dir/all' failed make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 Makefile:146: recipe for target `all' failed make: *** [all] Error 2 shahid Nayeem On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham mark.j.abra...@gmail.comwrote: For technical reasons

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

.dll' is not able to locate it. Please help me shahid Nayeem On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem msnay...@gmail.com wrote: Thanks. But when I ran make again I am getting this error [ 0%] Built target gmxfftw make[2]: *** No rule to make target `//cygdrive/c/packages/gromacs-4.6.3

[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%]

Re: [gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

: *** [all] Error 2 Please help me to compile gromacs 4.6.3 on cygwin Shahid Nayeem On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 10.09.2013 08:20, shahid nayeem wrote: I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs

[gmx-users] installing Gromacs4.6.3 on cygwin

Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%]

Re: [gmx-users] constant protonation state MD

. What is your system? A peptide? A globular protein? Best, Jesper On May 3, 2013, at 7:33 PM, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik and Baptista I am interested in simulating the change in secondary structure which is supposed to be influenced by the change in the pH

Re: [gmx-users] constant protonation state MD

, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from

Re: [gmx-users] constant protonation state MD

on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology

Re: [gmx-users] constant protonation state MD

does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation

[gmx-users] constant protonation state MD

Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- gmx-users

Re: [gmx-users] .top file from .tpr and .xtc

with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more

Re: [gmx-users] .top file from .tpr and .xtc

for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want

[gmx-users] topology

Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one of the CYS, SH in the form of SG as if it is involved in disulfide linkage, while the other chain with which I expect it to form disulfide link is not in the input pdb file. or can I use pdb2gmx command

Re: [gmx-users] topology

I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx. shahid On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 10:39 AM, shahid nayeem wrote: Hi All How can I get a topology file using pdb2gmx from a single chain polypeptide with one

Re: [gmx-users] .top file from .tpr and .xtc

to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components

Re: [gmx-users] boundwaters

, shahid nayeem wrote: Dear Users I am interested in knowing only the water molecules which remains bounded to the protein during MD. Using g_select I can make a boundwater.ndx file which gives water molecules within a specified distance from the protein but it gives different water molecule

[gmx-users] building_insertion_mutants

this protein and get the pdb of protein with inserted peptide segment. shahid Nayeem -- 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

[gmx-users] Generating insertion mutants

Dear all Please suggest me a tool with which I can generate insertion mutants from a .pdb file. I want to insert new 10-15 aa sequence of AA in between an existing .pdb file. The tool should write a new .pdb file with altered coordinates after insertion of new sequence and minimization of the

[gmx-users] LINCS

Dear all One basic clarification. How does LINCS algorithm influences the results of final production run. In what respect a minimization, pr and final simulation done with constraints = none and with constraint= all_bonds are different. Shahid Nayeem -- gmx-users mailing listgmx-users

Re: [gmx-users] LINCS

it computationally more expensive. Will these results will be O.K. Shahid Nayeem On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 2:02 PM, shahid nayeem wrote: Dear all One basic clarification. How does LINCS algorithm influences the results of final

Re: [gmx-users] LINCS

I want to simulate without building the missing residue. Does gromacs have an option of capping. I am using Gromacs 4.5.4. If not then suggest some software which I may use. Shahid nayeem On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 2:28 PM, shahid

[gmx-users] Generating_tpr_file from.xtc

Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Umbrella_pull_simulation

at http://www.freefilehosting.net/umbrellamut On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: The attached profile.xvg and histo.xvg are here. sorry for sending earlier mail without attachments Shahid Nayeem On Wed, Mar 7, 2012 at 3:25 PM, shahid

Re: [gmx-users] Umbrella_pull_simulation

-nBootstrap 200 -bsres bsResult_mut.xvg -bsprof bsprofile_mut.xvg -ac I get the values exactly opposite to my expectation and unable to find out where I am wrong please suggest. Shahid Nayeem On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem msnay...@gmail.com wrote: I have added some new windows

Re: [gmx-users] Umbrella_pull_simulation

for it. My profile.xvg and histo.xvg are right or they need more improvement. Shahid Nayeem On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value

Re: [gmx-users] Umbrella_pull_simulation

Thanks. But Does that mean that I should look in pullf.xvg of each window and see whether the value is converged or not. If not then I should extend the simulation. Shahid Nayeem On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My protein

Re: [gmx-users] Umbrella_pull_simulation

for equilibriation. Shahid Nayeem On Tue, Feb 21, 2012 at 6:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns for equilibriation. The new

Re: [gmx-users] Umbrella_pull_simulation

I thought this time to be sufficient without any reasonable basis. shahid Nayeem On Fri, Feb 24, 2012 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My system is a protein-protein complex. After pulling I selected windows at 0.1nm from an initial COM distance

Re: [gmx-users] Umbrella_pull_simulation

of the simulation required in each window with this information. Shahid nayeem On Fri, Feb 24, 2012 at 7:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I thought this time to be sufficient without any reasonable basis. If you pick an arbitrary time frame, you're going to get

Re: [gmx-users] Umbrella_pull_simulation

not getting smooth convergence. Shahid Nayeem On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem msnay...@gmail.com wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella

Re: [gmx-users] Umbrella_pull_simulation

Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it. Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul

Re: [gmx-users] Umbrella_pull_simulation

to you earlier. shahid Nayeem On Sat, Feb 18, 2012 at 7:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am doing umbrella sampling for a protein complex. After analysis I am finding that prifle.xvg has not converged. Now I want to extend simulation. I have

[gmx-users] Umbrella_pull_simulation

sampling. Please suggest. How one should ascertain the initial box size so that g_wham gives a converged profile.xvg. Please help. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] Umbrella_pulling_simulation

Dear All How does the terminal group capping/ionization state will influence the Free energy obtained from g_wham in umbrella sampling simulation. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Number of windows in umbrella sampling

histo.xvg and profile.xvg , it cost a lot computationally and if you don't get it right these computational resources are wasted. Shahid nayeem On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Thanks for quick reply. I have created mutant of a complex

Re: [gmx-users] Using shell script to analyze the results

Create a file named input.g_rms. write the group number in this file. In your shell script after command line write input.g_rms. when the command is executed in shell the file input.g_rms having group number will be read. Hope it works. Shahid nayeem On Fri, Feb 10, 2012 at 4:19 PM, Kiwoong Kim

[gmx-users] Running_crashed_run

in my case. Thanks for any help. Shahid Nayeem -- 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

[gmx-users] tip3p water in gromacs_4.5.4

. shahid Nayeem -- 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 interface or send

[gmx-users] topology and parameter for cobalt metal

respond. Please suggest where else I should search for these. Thanking all shahid Nayeem -- 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

Re: [gmx-users] RMSD

that I can compare side chain configuration of trajectory with bound and unbound sidechain configuration. Please help. Shahid Nayeem On Tue, Nov 15, 2011 at 7:02 PM, felmer...@uchile.cl felmer...@uchile.clwrote: In any case, if you really want to see flexibility then you need RMSF and not RMSD

[gmx-users] RMSD

Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] protein_model_refinement

. It is a big protein so long MD simulation is not possible. Short duration MD will be insufficient to search native structure. I am stuck-up. Can anyone on this list help me. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Protein_model_refinement

on this list to tell that how should I attempt this problem. Shahid Nayeem -- 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

Re: [gmx-users] Arginine_Hydrochloride topology

with protein. shahid nayeem On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine

Re: [gmx-users] Arginine_Hydrochloride topology

I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box shahid nayeem On Fri, Aug

Re: [gmx-users] Arginine_Hydrochloride topology

was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free

Re: [gmx-users] pmf_calculation

I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. shahid Nayeem On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem

Re: [gmx-users] pmf_calculation

Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood. On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I used following command

[gmx-users] Adding_topology_aminoacid

. shahid Nayeem -- 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 interface or send

[gmx-users] Arginine_Hydrochloride topology

Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. shahid Nayeem -- gmx

[gmx-users] pmf_calculation

two dips in PE curve. Please see it and tell me why I am getting these dips. Shahid Nayeem profile.xvg Description: Binary data -- 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

[gmx-users] pmf_calculation

Dear Justin Here is my histogram file which does not show any window overlap. The sampling window I choose was 0.2 nm which I think is very large. Please suggest. Shahid nayeem hist.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Thermal_Unfolding

this in gromacs then what should be the .mdp file for such increment in temperature at regular intervals. Thanks for any help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] binding_affinity

it does gives an oitput of summary_distance.dat. It has one column of conf.gro number but no distance. Where I am wrong. Shahid Nayeem On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What

Re: [gmx-users] binding_affinity

groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers

Re: [gmx-users] binding_affinity

Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. Shahid Nayeem On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify

[gmx-users] binding_affinity

Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem -- gmx-users

Re: [gmx-users] g_rms and g_cluster

for gromacs trajectory analysis where I can do backbone fitting first and then translate to coincide CA of residue of interest before calculating RMSD. Shahid Nayeem On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I want to calculate RMSD

[gmx-users] g_rms and g_cluster

clarification is that in gromacs g_cluster how can I use greedy algorithm for clustering. Shahid Nayeem -- 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

[gmx-users] backbone_few_sidechain_fixed

movement. In my posres.itp I used a force of 2000 kj to keep them in fixed position with option genrestr -fc. Waiting for reply Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] server_for_Gaussian

Dear All If any one is aware of a server on which one can upload job for running Gaussian, Please let me know. This I need to modify charges in the topology file created by ProDrg server. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] solvation_box_preparation

treatment of system then suggest me the way out. My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp are attached with this mail Shahid Nayeem On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Please tell me where I am wrong. I downloaded

[gmx-users] interface_enrgy

. Thanking you Shahid Nayeem -- 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] interface_enrgy

That means in energy group in .mdp file I should write interface.ndx and tell me if on interface there is hydrogen bond then its value I will get or not. Shahid Nayeem On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear User I am doing MD

Re: [gmx-users] solvation_box_preparation

potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. shahid nayeem On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham mark.abra...@anu.edu.au

[gmx-users] solvation_box_preparation

and pressure 100 bar, then 1ns simulated annealing from temp. 0k to 300k and then ins equilibriation at this temperature. In case of urea finally I got uniformly solvated urea_water_box but in chaps I couldn’t get it. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] solvation_box_preparation

warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote

[gmx-users] solvation_box

should I do. Shahid nayeem -- 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] solvation_box

but not inside water. I should have visualized it earlier before going for minimization. Please help me. shahid Nayeem On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/27/11, *shahid nayeem * msnay...@gmail.com wrote: Dear All I am trying to prepare

Re: [gmx-users] solvation_box

I forgot to mention that when I prepared urea_water box then also I got similar box of water in one region and urea in other region separated from it. But on minimization and following simulated annealing and equilibration I got a uniformly mixed urea water box. Shahid Nayeem On Thu, Jan 27, 2011

[gmx-users] preparation_solvation_box

Dear Gmx User I want to prepare a solvation box for say 50mM chaps solution. The density is not known. How should I start calculating the number of chaps molecule and number of water molecule required for say 6X6X6 size box, which after equilibriation should give the exact strength of the

[gmx-users] Interaction_between_protein_small_molecule

interaction between the two molecule. Please suggest me, how can I do this. Thanking you. Shahid Nayeem -- 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

[gmx-users] Terminal_ARG_residue causing problem in pdb2gmx

Dear Gromacs User My pdb is homodimer with Arg as c-terminal residue. With this pdb I am etting following error in pdb2gmx command Program pdb2gmx, VERSION 4.0.7 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms

Re: [gmx-users] heme

while running grompp. Please suggest me what should I do. Shahid Nayeem On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund er...@xray.bmc.uu.se wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx

[gmx-users] heme

parameter for these bonds but I couldnt get it. If someone on this mailing list can help me I will be grateful. Cyt C is very widely modelled protein with Gomacs in literature hence I expect to get some help from the forum. shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] heme

I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there. Shahid Nayeem On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C

[gmx-users] following_change_native_contact

Dear All How can I follow the changes in native contacts of protein unfolding trajectory. Is it g_mdmat, if so then how to analyze the results obtained from this command. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Heme_Grompp_error

in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Heme_Grompp_error

in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Grompp error: No default g96angle type

file shows these bonds the .gro file generated does not show these bonds in VMD while original pdb file shows these bonds. thanking you. waiting for your suggestion. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin These errors are from bond

[gmx-users] Heme_Grompp Error

in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Grompp error: No default g96angle type

) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. Thanks in anticipation of help. Shahid Nayeem -- gmx-users mailing list

Re: [gmx-users] Grompp error: No default g96angle type

for your suggestion to proceed further. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2

[gmx-users] g_sas

0.0234554 5 0.0284763 0.0401088 6 0.236609 0.108979 Tghe first column is atom no. and what are the values in two columns. I want average solvent accessible surface area of each atom of my protein in whole trajectory. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] do_dssp

as final.gro file shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx

Re: [gmx-users] do_dssp

Hi Justin I choose group 5 main chain for dssp calculation Shahid Nayeem On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file

Re: [gmx-users] do_dssp

Hi No i dont have any capping group shahid Nayeem On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I choose group 5 main chain for dssp calculation Do you have any capping groups (N-acetyl, C-amine, etc)? -Justin Shahid Nayeem On 5/24/10

[gmx-users] DSSP

/local/bin/ and I couldnt find. I even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] DSSP

backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded

Re: [gmx-users] DSSP

time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote

[gmx-users] xmgrace

Dear all I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands. tar -xvzf xmgr-4.1.2.tar.gz cd xmgr-4.1.2 ./configure make make install But it gives error command xmgr not found. Please help. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] protein Aggregation using Gromacs

Dear all What are the analysis tools which should be used on MD trajectory file in order to find potential aggregation sites of a protein. Anyone can tell me about specific resource material on use of Gromacs to predict protein aggregation hot spots from MD trajectory anlysis. Shahid Nayeem

Re: [gmx-users] protein Aggregation using Gromacs

. shahid Nayeem On 5/12/10, Ran Friedman r.fried...@bioc.uzh.ch wrote: Hi, There's no recipie to locate aggregation hot spots based on MD simulations. There are many papers on simulations of protein and peptide aggregation from which you can draw some ideas, but bear in mind that aggregation

[gmx-users] confusion about trjconv

with -cpi flag. I require answer of my question regardless of the use of .cpt file. shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

Re: [gmx-users] more than one peptide in one simulation box

wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular

Re: [gmx-users] more than one peptide in one simulation box

, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want

Re: [gmx-users] more than one peptide in one simulation box

Hi Justin Should I try to do position restraint at 500k and then full MD simulation. shahid On 4/27/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position

Re: [gmx-users] more than one peptide in one simulation box

Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. Shahid On 4/27/10, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three

[gmx-users] more than one peptide in one simulation box

than one residue in insert molecule. Please help me and write commands which I should follow. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

Re: [gmx-users] genbox

I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. msnayeem On 4/20/10, Justin A. Lemkul

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