[gmx-users] How to create S-S bond

Dear sir, I want to create S-S bond between two cys in a peptide chain irrespective of the conformation of the peptide. I tried this using an option -ss as flag in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more in free cysSH cysSH, but i want to bring them together to form

[gmx-users] How to create S-S bond

Dear sir, I want to create S-S bond between two cys in a peptide chain irrespective of the conformation of the peptide. I tried this using an option -ss as flag in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more in free cysSH cysSH, but i want to bring them together to form

[gmx-users] cannot determin precesion of .trn file

conv the same message have come but at different time steps. I am not getting what's happening. I am waiting for positive response with warm Regard Kinshuk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/

[gmx-users] peptide is going outside of box

Hi all, I have to simulate peptide with SPC water model.During the simulation trajectory peptide is some time going out of box through periodic boundary condition is there but physical prescence of solvent is not there, i mean if i have to extract water molecule within 3 angstrong cutoff of pept

[gmx-users] adding a polar Hydrogen atom to pdb file

any positive response. Kinshuk IIT-Bombay India ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problem regarding Complex ion addition by genbox

rcoulomb= 1.5 ; cut-off for coulomb >>> ;Temperature coupling >>> Tcoupl = berendsen; temperature bath >>> (yes,no) >>> ref_t = 298 298 >>> tc-grps = Protein Non-Prote

[gmx-users] X.gro file for different solvent system

ro.Is it a particular ratio between urea & water molecules for particular concentration ? If it is then this X.gro file (guanidium + thiocynate ion + water ) will be input for -cs flag in genbox for particular concentration in different size of box? Kinshuk Raj Sr

Re: [gmx-users] Problem regarding Complex ion addition by genbox

= no ; pressure bath >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Velocity generation >> gen_vel = yes ; generate initial >> gen_temp

[gmx-users] Problem regarding Complex ion addition by genbox

icular >> salt concentration how do i will perform it. >> > with genbox. compute number yourself. >> >> Kinshuk >> IIT-Bombay >> India >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >

[gmx-users] polyatomic ion additon by genion & genbox

with perticular >> salt concentration how do i will perform it. >> > with genbox. compute number yourself. >> >> Kinshuk >> IIT-Bombay >> India >> >> ___ >> gmx-users mailing listgmx-users@gromac

Re: [gmx-users] polyatomic ion additon by genion

salt concentration how do i will perform it. >> > with genbox. compute number yourself. >> >> Kinshuk >> IIT-Bombay >> India >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromac

Re: [gmx-users] problem regarding range checking error

Thanks for provoiding insight. I have gone through instructions for grompp for EM.I have gone through manual.I breakup the structure in manageable chunks i.e. i seperately run the EM & PR for SCN, GUD, Protein individally,every individual run was successful nothing get breakdown.As pr your's in

Re: [gmx-users] problem regarding grompp

thankful to you. KINSHUK > [EMAIL PROTECTED] wrote: >> Hi all, >> I have been trying to simulate peptide (octa alanine). In genbox i have >> inserted 40 molecule of guanidium ion & 800 water molecule (by -ci & >> maxsol option in gromacs 3.3.3)then again wit

[gmx-users] problem regarding grompp

Hi all, I have been trying to simulate peptide (octa alanine). In genbox i have inserted 40 molecule of guanidium ion & 800 water molecule (by -ci & maxsol option in gromacs 3.3.3)then again with genbox i added 40 molecules of thiocynate ion & 80 water molecules as above mentioned way. When i trie

[gmx-users] polyatomic ion additon by genion

atom by replacing water molecule it seems that genion is applicable only for monoatomic ion. If i have to do simulation with these polyatomic ions with perticular salt concentration how do i will perform it. Kinshuk IIT-Bombay India ___ gmx-users mai

[gmx-users] Proble while running minimization using .tpr file

Hi All, Myself Kinshuk from IIT-Bombay.I have gone through gromacs mailing list there i came to know about you while searching the solution of the problem while running minimization using .tpr in position restraints steps of MD run.I have been performing simulation of guanidium ion & phosphate

[gmx-users] x2top & Library file ffG43a1.n2t

file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable.) So how do i will be able to resolve this problem. If i will be getting any help i will be very thankful for you. Kinshuk Raj Srivastava IIT-Bombay India

[gmx-users] (no subject)

ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable.) So how do i will be able to resolve this problem. If i will be getting any help i will be very thankful for you. Kinshuk Raj Srivastava IIT-Bombay India

Re: [gmx-users] generation of guanidium intramolecular force-field

m is fixed and if i have to generate a system of different molal(different ratio of urea and water), so will be play with concentration. If any help i will be getting, i will be very thankful. kinshuk raj srivastava IIT-Bombay India Quoting [EMAIL PROTECTED]: > >> >> >>

[gmx-users] use of distance dependent dielctric

Hi all, i want to confirm whethere there is a distance dependent dielctric function in GROMACS.I want to use this. Please suggest me the possible sources. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] generation of guanidium intramolecular force-field

about file corresponding guanidium ion. I tried to make it with argenine side chain but i have been facing problem while generating above mentioned file. kinshuk raj srivastava IIT-Bombay Mumbai, India ___ gmx-users mailing listgmx-users@gromacs.org