Dear gmx users,
Dear Dr.Mark and Dr.David thank you
for your suggestion. I would like to use OPLS_AA force
field to my protein.
with best regards,
Nagaraju.
___
Dear gmx users,
In my protein instead of L-Alanine, I
would like to take D-Alanine. To this modification,
which parameters in L-Alanine to be modified to treat
as D-Alanine.
Any suggestion is appreciated. Thank you in
advance.
with best reg
Dear gmx users,
Dear Dr.Oliver as per your suggestion, I did
the modification of H atom type for POPE lipid
molecule. Here I am giving what I have done
modification in ffoplsaanb.itp file under [ atomtype ]
section.
(1) First I tried as given below
opls_963 CT
Dear gmx users,
I am trying to equilibrate POPE lipid
bilayer. As per mailing list
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html.),
C6/C12 parameters are converted into sigma/epsilon. I
modified " H " atom type to opls_369 in pope.itp
file(show below).
xxx
Dear gmx users,
I am thankful to Dr.Mark and Dr.Osmair for
their responce to my queries. As per their suggestion,
I checked ions.itp file in that sodium atoms are
represented by NA+ in opls force field. I am using
gromacs 3.3.1 version.
[moleculetype ]
; molname nrexcl
NA+
Dear gmx users,
I am trying to neutralize lipid bilayer with
Na ions by using genion command:
genion -f bilayer.tpr -o bilayer-Na.pdb -np 32 -pname Na -pq 1
Here is my bilayer.top file
#include "ffoplsaa.itp"
#include "pope.itp"
#include "dpopg.itp"
#include
Dear gmx users,
I built POPE+POPG (total 128 lipid molecules)
lipid bilayer in 3:1 ratio. POPE has neutral charge
and POPG has one unit of negative charge.To this lipid
molecules 3941 water molecules are added.
While creating bilayer.tpr file, it is giving non-zero
total c
Dear gmx users,
Dear Mark thank you very much for your suggestion. I
would like to do MD simulation at perticular pH. I think that in AMBER it is
possible but I have some problems regarding lipid bilayer parameters. Because
of this I would like to convert gromacs lipid
Dear gmx users,
I would like to use gromacs lipid
parameters in AMBER8.0 program. Is it posible to
convet lipid parameters downloaded from Dr.Tieleman
website to amber format. WOuld anyone has idea how to
convet pameters.
Any suggestion is appreciated.
Dear gmx users,
I downloaded POPE.itp and lipid.itp files from Dr.Tieleman
website http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
and POPG.itp file from Dr.Mikko Karttunen wesite
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml.
I built a POPE:POP
Dear gmx users,
I am very thankful to Dr.Oliver and Dr.Chris
Neale for their help.
with regards,
Nagaraju
-
Get the Yahoo! t
Dear gmx users,
I downloaded POPE.itp and lipid.itp file from Dr
Tieleman website http://moose.bio.ucalgary.ca/index.php?
page=Structures_and_Topologies. I am trying to convert C6/C12 parameters to
sigma/epsilon as suggestions given by Dr.Chris neale in mailing list
Dear gmx users,
I have some problem regarding scalling factor of cluster. Here I have given
cluster specifications, installation procedure, i request you go through query
and suggest me.
Here is the system specifications:
Master node: Intel Pentium 4, 3.0 GHz with 64HT 800 MHz FSB/2
Dear David,
Thank you for your suggestion. The file
attached in previous mail is corect but name is
different. I checked again using correct pdb file but
getting same problem. As per your suggestion, I am
submiting in bugzilla.
Thank you,
Dear gmx users,
I am trying to make index file for
POPG lipid molecule using the command:
make_ndx -f popg.pdb -o index.ndx
I am getting segmentation fault, but when i am
removing 53 atom in pdb file, i couldn't get
segmentation fault.
Here is the my pdb file:
CRYST1 95.707
Dear David and Stephan,
Thank you for your suggestion
and I will go through it. If i will get any problem, I
contact you.
with regards,
Ngaraju Mulpuri.
Dear gmx users,
I am using mdrun command in pentium-4
redhat linux, job was completed without any errors.
When I use the same files in cluster(redhat
enterprizes OS), I got the following error,
Grid: 14 x 14 x 15 cells
Configuring nonbonded kernels...
Testing x86_64 SSE2 support..
Dear Alan Dodd,
Thank you for your suggestion.
with regards,
Nagaraju
--
Dear gmx users,
I inserted mebrane protein in DOPC
lipid bilayer, some part of protein is outside of
lipid bilayer. Would you tell me how to add water
molecules to protein(to the out side of lipid bilayer
part) around 6 angstroms radius.
any suggestion is appreciated.
Dear Itamar,
Thank you for your suggestion, one more request, is any
tutorial available using this program.
with regards,
nagaraju
---
Dear gmx users,
would you tell me from where I can download
make_hole program, to insert protein in lipid bilayer.
Thank you i advance.
with best regards,
Dear gmx users,
I have one doubt regarding conversion of
C6/C12 parameters to sigma /epsilon.
I added atomtypes, pairtypes and dihedraltypes from
lipid.itp to ffoplsaanb.itp---after changing C6/C12
paramters to sigma/epsilon as given in mailing list
(http://www.gromacs.org/pipermail/
Dear gmx users,
I have one doubt regarding conversion of
C6/C12 parameters to sigma /epsilon. As Mr Chris neale said
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ), I added
atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb
Dear gmx users,
I have one doubt regarding conversion of
C6/C12 parameters to sigma /epsilon. As Mr Chris neale said
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ), I added
atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb
Dear gmx users,
I downloaded popc.itp file lipid.itp file from website
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. Based
on popc.itp file I prepared dopc.itp file for DOPC lipids. Here I have few
doubts.
1)
Dear gmx users,
I am trying to build DOPC lipid bilayer
using genconf command. The head groups in bilayer are
not coming in horizontal position. i.e all head groups
are coming like as slop.
here i am giving commands and options used to build a
bilayer:
editconf -f dopc_min.pdb -o dop
u want to
use, but the best way to tackle this (and the most didactical) is to
draw DPPC and/or POPC and indicate all atom names, numbers, types and
charges, bonds, pairs, angles, dihedrals and improper dihedrals. Then,
draw your DOPC and do the same, taking the same types for
corresponding atoms, bo
Dear Gromacs Users,
I searched mailing list for DOPC lipid bilayer
paramters. I found in one of the mailing list "For CHARMM parameters (which I
believe Feller uses), there is POPC in top_all27_prot_lipid.rtf. For the united
atom lternativ
28 matches
Mail list logo
