[gmx-users] flexiblity

Dear all I have simulated two different proteins (A and B). I need to compare their flexibility. RMSF help to examine their flexibilty individually, but I want to campare them with each other. Do anybody know a solution to this? Would you please help me in this regard? Regards Shiva -- gmx-users

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 209

> Message: 1 > Date: Tue, 31 May 2011 06:56:16 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] flexiblity > To: Discussion list for GROMACS users > Message-ID: <4de4c950.70...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed

[gmx-users] Labeled protein

Dear Justin I have prepared the pdb structure of an organic compound. This compound is applied as a lable which covalently and specifically attaches to a Cys residue of our protein. I want to attache the label to the protein and simulate this complex. what I need to know is that Can I manualy attac

[gmx-users] Labeled protein

shiva birgani wrote: > Dear Justin > I have prepared the pdb structure of an organic compound. > This compound is applied as a lable which covalently and specifically > attaches to a Cys residue of our protein. > I want to attache the label to the protein and simulate this complex

[gmx-users] xpm2ps

hi all dear I have used dssp to examine secondary structure of a protein. it have been done correctly but when I convert .xpm file to .eps the y-axis is so short and the numbers of residues are not distinguishable and the picture is not so clear !!! I wnat to know if there exist a way to change it

[gmx-users] Crashed run

Dear Justin I had a crashed run and continued it by tpbconv and mdrun. After that in order to analysis the results of new MD run I used of this command trjcat -s md2.tpr -settime But when I want to compute RMSD, DSSP, ... I do not know how I can put together the results of MD1 (crashed run) and MD2

[gmx-users] crashed run

Dear friends Thanks for help I did what you said. but now I have another question. why when I compute RMSD, there is a turbulence in the digits between two MD runs (MD1 & MD2)? Along 10nS RMSD values increase but after that in continued MD RMSD values start with lower digits. So the obtained RMSD

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 64

Dear Justin So thanks for your help. you are right. I had put a wrong .rtp file With regards Shiva -- 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 postin

[gmx-users] RMSF or RMSD per residues

Dear all I want to analyze the mobility of residues in various conditions. I need to know examining the RMSF is more useful or RMSD per residue? Thanks in advance Shiva -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] error in equilibration

Dear Justin I fallowed your tutorial of "Protein-Ligand Complex" to simulate a peptide associated with acetic acid. All the step was good but in Equilibration phase 1 I encountered with this error WARNING 1 [file nvt.mdp, line unknown]: Unknown left-hand 'continuation' in parameter file checkin

[gmx-users] field-specified name for sulfate

Hi All I am trying to add sodium sulfate to the system but I receive this fetal error Fatal error: No such moleculetype SO4 Could anybody tell me what is the force field-specified name of sulfate ion in OPLS-AA/L all-atom force field? regards, Shiva -- gmx-users mailing listgmx-users@groma

[gmx-users] salt bridge

Hi I want to see specific salt bridge residues for example which Arg by Glu is in salt bridges. But in step we got a list pairs in which Cl ions (Cl ions added to neutralize peptide in solvent by genion) are paired to residues. I don't know what is the problem and how can I have salt bridge residue

[gmx-users] simulation in the high temperature

Dear Justin I want to simulate a protein in the high temperature (338 K). I wan to know changing of ref_t in mdp file is enough and there is not any other parameter to be changed in this regard? and how much the results of this type of simulation (in high temperature) is reliable? thanks in advance