[gmx-users] Gromacs tutorials for binding free energy analysis

Hello dears I would liked to know which of the tutorials presented by Gromacs for binding free energy analysis (http://www.gromacs.org/Documentation/Tutorials)  are based on LIE method? regards, Sajad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm

[gmx-users] Lie method for binding free energy calculations

Hello dears  searching through literature, many cases of LIE method application for BFE   calculation of small molecules are on hand . but I couldn't find any report of using this method for interaction of small peptides and proteins. I wanted to know if the protocol prepared in Justin tutorial

[gmx-users] van der waals interaction

Dear users, Is there any way to find out About Van Der Waals interactions between two group of residues, by Gromacs? regards, sajad -- 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/M

[gmx-users] cutting a trajectory and continuing from a part of it

Dear users is there any way I can omit a part of my run and continue again from there on? in fact my protein escaped the box i had introduced to it, after 13ns past. I am searching for a way to bring it back and continue  my run after 13th ns. I do appreciate your kind help. regards, sajad-- gmx

[gmx-users] analyzing protein conformation stability

Hello Dear users is there any command in gromacs for analysis of protein stability? or I should be using those related to calculation of B-factor? best regards, sajad-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] -shell option of g_hbond

Dear users how can I use -shell option with g_hbond command? I wish to find h-bonds around a particular atom in a definite distance. how can I  introduce the index file and cut off distance to it? regards sajad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] distance between mass center of two groups

Dear users, is there any command in Gromacs to show fluctuations of distance, between mass center for two groups of amino-acids in  a protein, over time? thanks,  sajad-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] polt of eigenvector change for a residue

Dear users how can i have the plot whitch shows a perticular eigenvalue changes, for my protein residues? regards, sajad-- 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

[gmx-users] protein mass center

hi dear users is there any command in gromacs to determine mass center of a protein? I mean to find out witch atom or residue stands for mass center. thanks, sajad-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] gromacs make error

dear users while installing gromacs and after running ./configure, i tried to run the "make" command. but soon i was faced with an error witch is typed below. it seems that fftw libraries are not found. i downloaded and installed fftw3.2.2 as mentioned in gromacs website. and put the extracted

[gmx-users] simulation of a non complete structure

dear users is it rational to do a simulation on a structure witch is not complete? i mean pdb structure doesn't cover whole of the protein but it's active core domain. may be i should be asking this question somewhere else, but i thought some of you may have concerned with such case and in fact i

Re: [gmx-users] MG-ATP

So having a ATP-MG-complex in your simulation shouldn't be a problem. Regards, Felix Von: gmx-users-boun...@gromacs.org im Auftrag von Sajad Ahrari Gesendet: Mi 27.04.2011 10:52 An: gromacs user forum Betreff: [gmx-users] MG-ATP dear users is "MG-ATP

[gmx-users] MG-ATP

dear users is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, apart from each other and not being crystallized in the right place. can i omit them and replace ADP's with MG-ATP? or I should introduce this topology to gromacs? regards sajad -- gmx-users mailing listgmx-use

Re: [gmx-users] dealing with ATP

DONE STOP From: Justin A. Lemkul To: Gromacs Users' List Sent: Sat, April 23, 2011 5:46:24 PM Subject: Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > tnx for your help Justin! > but shouldn't the topology of S atom be described f

[gmx-users] introducing ADP and ATP to Gromacs

dear users is there any way to introduce "ADP" and "ATP" to Gromacs? my protein holds these ligands. but they are not known to Gromacs. regards. Sajad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.g

Re: [gmx-users] dealing with ATP

users Sent: Sat, April 23, 2011 5:54:58 AM Subject: Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > Dear users > i am working with a protein witch holds a hetero-atom in it's pdb structure. >the hetero-atom  is named "d" and stands for "ADP+SO4" (in fac

[gmx-users] dealing with ATP

Dear users i am working with a protein witch holds a hetero-atom in it's pdb structure. the hetero-atom  is named "d" and stands for "ADP+SO4" (in fact the third phosphate of ATP is being substituted with SO4). i wanted to know if gromacs holds a feature to change "d" into ATP? and if so do i n

[gmx-users] how to deal with xleap to simulate a protein-ligand complex?

dear users in order to simulate a Kinase protein attached with two ligands (MG and ATP in particular), i am trying to use amber03 force field with xleap in amber10 (based on some relevant litratures). in fact i am going through a tutorial introduced by Justin Lemkul, entitled "protein ligand co

[gmx-users] fetal erorr while running" pdb2gmx" command

dear users after running the command "pdb2gmx -f 1OL5.pdb -o 1OL5.gro -water spc" ,i was faced with the erorr: "Fatal error: Atom CG not found in residue seq.nr. 251 while adding atom". i used Gromacs 4.5.3 with AMBER99SB force field. it seems that some atomes are missing.should i be modeling th

Re: [gmx-users] erorr while using grep command

. Furthermore, to omit TPO, you need to run grep -v 'TPO' 10L5.pdb > No-TPO.pdb Hope it helps, Tsjerk On Sun, Apr 17, 2011 at 12:09 PM, Sajad Ahrari wrote: > hello every one! > I am trying to omit TPO(witch stands for phospho-tyrosine) from my pdb file > by executing the com

[gmx-users] erorr while using grep command

hello every one! I am trying to omit TPO(witch stands for phospho-tyrosine) from my pdb file by executing the command"grep TPO 10L5.pdb > TPO.pdb". but i am being facing with this erorr"grep: 10L5.pdb: No such file or directory" can any one help?-- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] suitable forcefield

dear users I going to simulate a Kinase protein with "MG_ATP" as co-factor. do you have any idea witch force field of Gromacs4.5.3 would be most suitable? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

[gmx-users] drawing the plots

hello dear Gromacs users i have Gromacs4.5.3 installed on suse11.1.but when i run commands like" g_gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg"i can't see any plot drawn. although the command is run with no error. by the way i have the package "package xmgrace-5.1.21-27.91.x86_64" al