[gmx-users] density map calculation of lipid around 10 angstrom of protein

hello i am trying to calculate 2D number-density maps of lipid around 10 angstrom of protein. My system consist both coarse grained protein and lipid (using martini force field).the command is gmx densmap -f *.xtc -s *.tpr -n *.ndx -aver z -bin 0.02 -xmin -1 -xmax -1 -o *.xpm but the error i am

Re: [gmx-users] question regarding gmx helix orientation

: > > > On 12/13/19 7:06 AM, SHAHEE ISLAM wrote: > > Yes ,I am using cg model. > > Use gmx gangle. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall &g

Re: [gmx-users] question regarding gmx helix orientation

Yes ,I am using cg model. On Dec 13, 2019 2:37 PM, "Alessandra Villa" < alessandra.villa.bio...@gmail.com> wrote: Hi, On Thu, Dec 12, 2019 at 1:09 PM SHAHEE ISLAM wrote: > hi, > i want to calculate the tilt angle of helix against the bilayer normal. > First i made a

[gmx-users] question regarding gmx helix orientation

hi, i want to calculate the tilt angle of helix against the bilayer normal. First i made a index file which contains the backbone of the residues of large helix. I am using this command *gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise -oradius -otwist -obending -otilt -orot*

[gmx-users] calculation of tilt angle of helix against the bilayer normal

hi, i want to calculate the tilt angle of helix against the bilayer normal. iam using this command *gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise -oradius -otwist -obending -otilt -orot* my question 1. how can i calculate the angle, so that angle can be calculated against

Re: [gmx-users] calculation of cross sectional area of protein on lipid

thank you so much for your guidance. On Wed, Nov 6, 2019 at 6:41 PM Justin Lemkul wrote: > > > On 11/6/19 8:03 AM, SHAHEE ISLAM wrote: > > hi, > > i want to calculate the cross sectional area of protein on the lipid > layer. > > Can anyone please guide me how can

[gmx-users] calculation of cross sectional area of protein on lipid

hi, i want to calculate the cross sectional area of protein on the lipid layer. Can anyone please guide me how can i do that. By using gmx sasa i can calculate the surface area of protein. What should i choose so that i can calculate cross section area of protein on lipid bilayer. thanking you

Re: [gmx-users] how to select head groups of lipid within 10 angstrom of protein

i am doing this simulation with martini coarse grained force field. so i just replace p and n by bead name and it is working now. thank you so much again for your reply. On Wed, Oct 30, 2019 at 1:04 PM SHAHEE ISLAM wrote: > i am so sorry for the late reply. I have applied both of y

Re: [gmx-users] how to select head groups of lipid within 10 angstrom of protein

gt; > > Sent from my iPhone > > > >> On Oct 25, 2019, at 11:45 AM, SHAHEE ISLAM > wrote: > >> > >> Hi, > >> I am trying to calculate the angle between P and N vector of my lipid > >> (popc+popg) with regards to the z axis to see how the protei

[gmx-users] how to select head groups of lipid within 10 angstrom of protein

Hi, I am trying to calculate the angle between P and N vector of my lipid (popc+popg) with regards to the z axis to see how the protein is affecting the membrane. I am using this command, but it does not working gmx select -f *.xtc -s *.tpr -select POPG & name P* N* within 1.0 of Protein -oi

[gmx-users] inter-residue contact map

hello, i want to calculate the contact map between two different proteins. Using mdmat it is possible to calculate the contact map within a protein. But can anyone please suggest me how i can calculate the inter-residue contact map between two proteins using gromacs. thanking you shahee --

[gmx-users] error: during simulation of martini cg membrane protein

hi, i am following charmm gui martini maker to prepare a membrane protein cg system.My system consist of one protein(consist of 129 amino acid), popc bilayer(no of lipid 256), water and ions.The minimization steps go well.But during the equilibration simulation stoped with this error.(here i am

Re: [gmx-users] calculation of pair wise interaction energy of residues

ay. > > Mark > > On Tue, 16 Apr 2019 at 07:52, SHAHEE ISLAM wrote: > > > hi, > > Is it possible to calculate pair wise interaction energy of each residue. > > My protein consist of 129 residue. Because if i mention each residue as a > > group in mdp file

[gmx-users] calculation of pair wise interaction energy of residues

hi, Is it possible to calculate pair wise interaction energy of each residue. My protein consist of 129 residue. Because if i mention each residue as a group in mdp file then i will get a huge number of data. Which is very difficult to handle. Can anyone please suggest me how i can do this.

[gmx-users] how to create a index file for angle calculation

hi, if i want to calculate angle between two group,then the group will be in same file or in different file.because when i am using this command gmx gangle -f md-0-1-300k-pbc.xtc -n index.ndx -dt 2000 -oall angle.xvg putting the two group (1 and 2 both) in same idex file , i am getting the values

Re: [gmx-users] calculate interaction energy between two proteins

thank you so much. now i understand this. On 1/9/19, Justin Lemkul wrote: > > > On 1/9/19 3:31 AM, SHAHEE ISLAM wrote: >> it is connected with aggregation phenomenon. > > Maybe, but no force field is parametrized with protein aggregation in > mind. Mark is cautioning you

Re: [gmx-users] calculate interaction energy between two proteins

it is connected with aggregation phenomenon. On 1/9/19, Mark Abraham wrote: > Hi, > > How is the protein-protein interaction energy defined? What physical > observable is it connected to? > > Mark > > On Wed, Jan 9, 2019 at 9:03 AM SHAHEE ISLAM wrote: > >> can a

[gmx-users] calculate interaction energy between two proteins

-Protein58 Lamb-W 59 Lamb-ION if i select 42 and 43. will it give me the total energy value considering both proteins. or what should i correctly select. thanking you Shahee Islam -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] calculate angle between two beeta sheet

can anyone please help me in this regards. On 1/4/19, SHAHEE ISLAM wrote: > hi, > my protein contain three beeta sheet. > (i) resid 43-45 > (ii) resid 51-53 > (iii) resid 58-59 > i want to calculate the angle between two beeta sheet.can any one > please suggest me how i ca

[gmx-users] calculate angle between two beeta sheet

hi, my protein contain three beeta sheet. (i) resid 43-45 (ii) resid 51-53 (iii) resid 58-59 i want to calculate the angle between two beeta sheet.can any one please suggest me how i can do this. thanking you shahee -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] how to restart a job in grmacs

if i want to store 10-15 ns .xtc file in a different .xtc file then what should i do. thanking you On 12/27/18, SHAHEE ISLAM wrote: > thank you so much. > > On 12/27/18, sp...@iacs.res.in wrote: >> - Message from SHAHEE ISLAM - >>     Date: Thu, 27 De

Re: [gmx-users] how to restart a job in grmacs

thank you so much. On 12/27/18, sp...@iacs.res.in wrote: > - Message from SHAHEE ISLAM - >     Date: Thu, 27 Dec 2018 16:52:17 +0530 >     From: SHAHEE ISLAM > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] how to restart a job in grmacs >

Re: [gmx-users] how to restart a job in grmacs

thank you is the trajectory wil be from 0-15 ns or it will be from 10-15 ns. On 12/27/18, sp...@iacs.res.in wrote: > - Message from SHAHEE ISLAM - >     Date: Thu, 27 Dec 2018 16:41:21 +0530 >     From: SHAHEE ISLAM > Reply-To: gmx-us...@gromacs.org > Subject: Re:

Re: [gmx-users] how to restart a job in grmacs

thank you so much for your reply. -extend 5000 what does it signify.if the time step is 2 fs then by simply multiplying these two it will give 10 ns. thanking you On 12/27/18, sp...@iacs.res.in wrote: > - Message from SHAHEE ISLAM - >     Date: Thu, 27 Dec 2018 16:16:18

[gmx-users] how to restart a job in grmacs

hi, i have run a simulation for 10 ns but after 4 ns due to power off the job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi md_0_10ns.cpt,continue the left simulation.Now after normal termination of 10 ns how i wll do the next 5 ns simulation after this 10 ns. thanking you shahee --

Re: [gmx-users] contact analysis between the all backbone of same protein

ffs are 1.1 nm. > > > Peter > > On 19-12-18 09:30, SHAHEE ISLAM wrote: >> thank you so much for your reply. >> I have done according your instruction.Can you please tell me what >> should best cut off for martini coarse grained force field. >> thanking you >> s

Re: [gmx-users] contact analysis between the all backbone of same protein

thank you so much for your reply. I have done according your instruction.Can you please tell me what should best cut off for martini coarse grained force field. thanking you shahee On 12/18/18, soumadwip ghosh wrote: > Hi, > > You can obtain the backbone atom contacts in the same protein using

[gmx-users] contact analysis between the all backbone of same protein

hi, to calculate the contact between the all backbone of a protein ,is the following command is correct gmx mindist -f dynamic.xtc -s equilibration.gro -n bb-p.ndx -dt 1000 -d 0.5 -on contact.xvg -od mindist.xvg because after entering this command i have to select the same group for two times.

Re: [gmx-users] contact analysis within the all backbone of a protein

can anyone please tell me is this correct or how i can do this. On 12/17/18, SHAHEE ISLAM wrote: > hi, > to calculate the contact between the all backbone of a protein ,is the > following command is correct > gmx mindist -f dynamic.xtc -s equilibration.gro -n bb-p.ndx -dt 1

[gmx-users] contact analysis within the all backbone of a protein

hi, to calculate the contact between the all backbone of a protein ,is the following command is correct gmx mindist -f dynamic.xtc -s equilibration.gro -n bb-p.ndx -dt 1000 -d 0.5 -on contact.xvg -od mindist.xvg because after entering this command i have to select the same group for two times.

Re: [gmx-users] secondary structure analysis

lation either a) you did something wrong or b) your looking at an > analysis artefact. > > Martini is not the right tool to study SS changes. > > Peter > > > On 25-09-18 09:13, SHAHEE ISLAM wrote: > > by using only the .gro is it possible to calculate the secondary >

Re: [gmx-users] secondary structure analysis

by converting cg.gro to all atom gro file.) i cant use the .xtc file ,because it is a martini cg.xtc file. thanking you shahee On 9/24/18, SHAHEE ISLAM wrote: > thank you so much for your quick reply.if i convert the coarse grained > pdb into all atom gro file,then vmd can calculate the sec

Re: [gmx-users] secondary structure analysis

., 2008, > DOI:10.1021/ct700324x. > > From: Soham Sarkar > Sent: 24 September 2018 14:10 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] secondary structure analysis > > You can use do_dssp utility to generate the secondary structure > > On Mon, 24 Sep 2018, 5:34 pm S

[gmx-users] secondary structure analysis

hi, i am doing martini based coarsed coarse grained simulation in gromacs.after getting the coarse grained structure ,i can convert cg pdb it to the gro file.using vmd, seondary structure can be analysed.can any one suggest what may be the best way to calculate the secondary structure change of

[gmx-users] secondary structure analysis

hi, i am doing martini based coarsed coarse grained simulation in gromacs.after getting the coarse grained structure ,i can convert cg pdb it to the gro file.using vmd, seondary structure can be analysed.can any one suggest what may be the best way to calculate the secondary structure change of

Re: [gmx-users] name of the residue contact between two proteins

where i have calculate the no of contact analysis by this commands gmx mindist -f md.xtc -s eq.gro -n index.ndx -dt 1000 -d 0.5 -on numcount.xvg -od mindist.xvg On 6/26/18, SHAHEE ISLAM wrote: > hi, > i have two protein in a system.i have already calculate the no of > contacts be

[gmx-users] name of the residue contact between two proteins

hi, i have two protein in a system.i have already calculate the no of contacts between two proteins. now i want to caculate the name of the residues which are in the contact within 5 angstrom of the two protein. i.e the name of residues of protein1 which are in the contact with the residue name of

[gmx-users] analysis of angle between two beta sheet of martini protein cg

hi, i want to calculate the angle between the two beeta sheet of a protein.for this reason i have made a index file containing two beeta sheet group.can anyone please suggest me how can i do this. i am using this command gmx gangle -f ../pbc340.xtc/md-340k-0-1 -s ../equilibration.gro -n

[gmx-users] angle calculation

hi, i want to calculate the angle between the two beeta sheet of a protein.for this reason i have made a index file containing two beeta sheet group.can anyone please suggest me how can i do this. i am using this command gmx gangle -f ../pbc340.xtc/md-340k-0-1 -s ../equilibration.gro -n

Re: [gmx-users] secondary structure query

thank you sir,for your suggestion.yes the error was because of version mismatch. On 6/12/18, Justin Lemkul wrote: > > > On 6/12/18 9:31 AM, SHAHEE ISLAM wrote: >> hi, >> i am following this tutorial >> http://cgmartini.nl/index.php/tutorials-general-introduction/pro

Re: [gmx-users] secondary structure query

annot read anything but the biomolecules. > > On Tue, 12 Jun 2018, 7:01 pm SHAHEE ISLAM, wrote: > > > hi, > > i am following this tutorial > > http://cgmartini.nl/index.php/tutorials-general-introduction/proteins. > > afrter converting the coarse grained protein to all at

[gmx-users] secondary structure query

hi, i am following this tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/proteins. afrter converting the coarse grained protein to all atom structure by charmm force field,i have gotten the all atom gro file.now i want to analyse the secondary structure of thih gro file. when

Re: [gmx-users] regarding rmsd calculation

sorry to forget about the recentering of the .xtc file.after getting the dynamic.xtc file i just recenter the .xtc file before doing rmsd analysis. On 6/5/18, SHAHEE ISLAM wrote: > hello sir, > there are two proteins in a water box system.i am doing martini > protein cg simulation and

Re: [gmx-users] regarding rmsd calculation

mdrun -deffnm dynamic1 -v from the visual inspection there is not that much of difference between the two .xtc file. did i have done any wrong for the continuity of the simulation. thanking you shahee On 6/4/18, Justin Lemkul wrote: > > > On 6/4/18 8:57 AM, SHAHEE ISLAM wrote: >> hi

[gmx-users] regarding rmsd calculation

hi, i am doing thr rmsd calculation of protein,by using the command gmx rms -n ../ndx/index-p1-0-1.ndx -s ../dynamic.tpr -f ../pbc.xtc/md-0-1.xtc -o rmsd-p1-0-1.xvg -tu ns (this is for first 1 microsecond) then again i have done for the next 1 micro second gmx rms -n ../ndx/index-p1-0-1.ndx -s

Re: [gmx-users] backbone contact analysis of martini cg protein

can anyone please give me some idea. On 5/30/18, SHAHEE ISLAM wrote: > hi, > i want to calculate the contact between the backbone of protein(it is > a coarse grained protein using martini force field).how i will make > .ndx file to calculate the contact. > > thanking

[gmx-users] backbone contact analysis of martini cg protein

hi, i want to calculate the contact between the backbone of protein(it is a coarse grained protein using martini force field).how i will make .ndx file to calculate the contact. thanking you shahee islam university of calcutta -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] how to select backbone of martini protein cg

i have followed this tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/proteins On 5/29/18, SHAHEE ISLAM wrote: > hi, > i want to calculate the contact between the backbone of protein(it is > a coarse grained protein using martini force field).how i will make &g

[gmx-users] how to select backbone of martini protein cg

hi, i want to calculate the contact between the backbone of protein(it is a coarse grained protein using martini force field).how i will make .ndx file to calculate the contact. thanking you shahee islam university of calcutta -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

thank you so much for your reply. On 5/28/18, Soham Sarkar <soham9...@gmail.com> wrote: > use the latest .tpr formed after production run else try > > tpbconv -s dynamic.tpr -o dynamic_new.tpr > > On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM <islamsha...@gmail.com>

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

file with tpbconv. On 5/28/18, SHAHEE ISLAM <islamsha...@gmail.com> wrote: > after deleting -select > this error is coming > Invalid command line argument: > cog of group "Chain_A" plus cog of group "Chain_B" > > > On 5/28/18, Soham Sarkar <

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

after deleting -select this error is coming Invalid command line argument: cog of group "Chain_A" plus cog of group "Chain_B" On 5/28/18, Soham Sarkar <soham9...@gmail.com> wrote: > Delete from -select.. previous are ok > > On Mon, 28 May 2018, 3:12 pm SHAHEE I

[gmx-users] calculation of distance between the center of geometry of two proteins

e in this index file the two chain group name Chain_A and Chain_B how i will select the two chain. thanking you shahee islam university of calcutta -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

Re: [gmx-users] regarding rmsd calculation of protein

ave > > On Thu, 24 May 2018, 11:26 am SHAHEE ISLAM, <islamsha...@gmail.com> wrote: > >> Really thank you so much for your reply. >> can i select the two chain at a time.because both protein contain 120 >> amino acid respectively. >> then >> > ri

Re: [gmx-users] regarding rmsd calculation of protein

ENAME CHAIN_A Group is empty On 5/24/18, Soham Sarkar <soham9...@gmail.com> wrote: > You should give like ri 1-120 > > On Thu, 24 May 2018, 11:14 am SHAHEE ISLAM, <islamsha...@gmail.com> wrote: > >> yes its working. >> now >> >ri ( give numbers for resi

Re: [gmx-users] regarding rmsd calculation of protein

gt; Put L(small) > It will give the residue number > > On Thu, 24 May 2018, 11:00 am SHAHEE ISLAM, <islamsha...@gmail.com> wrote: > >> after giving this command >> make_ndx -f em.gro -o index.ndx >> nr : group ! 'name' nr name 'splitch' nrEnter: list groups >

Re: [gmx-users] regarding rmsd calculation of protein

Sarkar <soham9...@gmail.com> wrote: > It is any .gro file of your system > You can make index file after final md > > On Thu, 24 May 2018, 10:37 am SHAHEE ISLAM, <islamsha...@gmail.com> wrote: > >> you have mention here em.gro,i think it is a gro file of >

Re: [gmx-users] regarding rmsd calculation of protein

you have mention here em.gro,i think it is a gro file of equilibration.can i make the index file after production run to calculate rmsd. On 5/23/18, SHAHEE ISLAM <islamsha...@gmail.com> wrote: > thank you so much for your quick reply. > > On 5/23/18, Soham Sarkar <soham9..

Re: [gmx-users] regarding rmsd calculation of protein

e them as Chain_A and Chain_B >>v (shows the newly indexed file) >>q (save) > Now your index has two chain seperated > > On Wed, May 23, 2018 at 5:54 PM, SHAHEE ISLAM <islamsha...@gmail.com> > wrote: > >> hi, >> i have two protein in my gro

[gmx-users] regarding rmsd calculation of protein

elements for this reason i am able to calculate the rmsd of two protein together by selecting 1. but i want to calculate the rmsd of the protein individualy.how i will do this. My .gro file consist of atom no 1 to 283 for protein1 and atom no 284 to 566 for protein2. thanking you shahee islam university

Re: [gmx-users] secondary structure analysis

sider upgrading to (the much faster) gromacs 2018. > > On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM <islamsha...@gmail.com> > wrote: > >> i have installed dssp2.04 in usr/local/bin. >> >> On 5/16/18, Joe Jordan <e.jjorda...@gmail.com> wrote: >> > You have to

Re: [gmx-users] secondary structure analysis

i have installed dssp2.04 in usr/local/bin. On 5/16/18, Joe Jordan <e.jjorda...@gmail.com> wrote: > You have to point to where you have dssp installed. This may require you to > install dssp. > > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM <islamsha...@gmail.com> > w

[gmx-users] secondary structure analysis

i want calculate the secondary structure of protein in gromacs.but when i am using this command do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10 getting this error Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572

Re: [gmx-users] installion of gromacs 5.07

gt; > Please consider installing a recent version of GROMACS, which is not only > easier to use and install but is still supported and will have fewer bugs, > too. Either way, you will need to use a more recent compiler than you seem > to have available on your system. > > Mark

[gmx-users] Fwd: installion of gromacs 5.07

-- Forwarded message -- From: SHAHEE ISLAM <islamsha...@gmail.com> Date: Tue, 17 Apr 2018 16:16:41 +0530 Subject: installion of gromacs 5.07 To: gromacs.org_gmx-users@maillist.sys.kth.se hi, i am just new of gromacs.I want to install the gromacs 5.07.I am following this tu

[gmx-users] installion of gromacs 5.07

hi, i am just new of gromacs.I want to install the gromacs 5.07.I am following this tutorial http://www.gromacs.org/Documentation/Installation_Instructions_5.0 at first i have install cmake3.2.0.then follow this tar xfz gromacs-5.0.7.tar.gz cd gromacs-5.0.7 mkdir build cd build cmake ..