[gmx-users] Unsupported box diagonal

Hi, I am trying to do a simple membrane simulation of a h4 residue helix in DMPC. However, I encounter a strange issue this time when i try to run the final production run. the error that i get is as follows: Check for bad contacts and/or reduce the timestep. WARNING: Unsupported box diagonal 6.1

[gmx-users] gmembed

Hi, I am trying to insert my protein dimer complex in a membrane using the g_membed tool. I made an index group where I saved the monomers as separate groups and mentioned the same groups in the .mdp file. However, it gives me an error saying "Freeze value does not match :There are 2 freeze groups

[gmx-users] inflate gro

Hi, I am trying to use inflategro to efficiently insert my protein into lipid bilayer. I have been following the KALP-15 in DPPC tutorial to do so. However, after running the perl script for the first time, I am not able to perform energy minimisation. The error message that I get when I pre proc

[gmx-users] Re: inflate gro

Hi Justin, Thanx for the suggestion. This is how my topology looks like with the strong position restraint included for the protein: ; Include forcefield parameters #include "gromos53a6.ff/forcefield.itp" ; Include chain topologies #include "complex6_Protein_chain_X.itp" #include "complex6_Prote

[gmx-users] protein in membrane

Hi, I used the inflategro.pl script to insert my protein into the membrane and scaled down the lipids until it reached the recommended area per lipid value. After removing 4 lipid molecules, I started with an area of 90 square angstrom and reached a value of 65 square angstrom within just 5 iterat

[gmx-users] atom type not in rtp entry

Hi, I get the following error message when i try to pdb2gmx my protein file: Fatal error: Atom D21 in residue LEU 1 was not found in rtp entry LEU with 11 atoms while sorting atoms. I wonder which of these need to be changed! Thank you for your time. ___

[gmx-users] atom type OXT

Hi all, I have been trying to pdbgmx my protein to obtain the gro and top files as follows: pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter -ignh However, I get an error message that states: Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms while sorting atoms I f

[gmx-users] Re: atom type OXT

> Message: 4 > Date: Tue, 06 Sep 2011 22:35:09 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] atom type OXT > To: Discussion list for GROMACS users > Message-ID: <4e66137d.9040...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >

[gmx-users] Strangeness in gro file

Hi all, I am trying to use the g_membed tool to insert my protein into a DMPC membrane. My protein is a dimer and hence I separated the two monomers by a TER card in the original pdb file before pdb2gmx step for gromacs to identify it as teo separate entities.. I then merged my protein file with

[gmx-users] Re: strangeness in gro file

p 2011 16:12:49 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] Strangeness in gro file > To: Discussion list for GROMACS users > Message-ID: <4e6ef461.7000...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 13/09/2011 3:27 PM, Swet

[gmx-users] Membrane protein simulation

Hi, I embedded my protein of interest into a DMPC membrane by the g_membed tool with the following command: g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100 I then energy minimized the resultant structure for 1 ns before the position

[gmx-users] Problem with using topolbuild1_3.tgz

Hi, I am trying to generate topology files for a set of lipids with the help of topolbuild1_3.tgz package found at the other software page of GROMACS website. I downloaded and installed all files and tried running the program with a MOL2 file with charges in it. However, it shows an error message

[gmx-users] Re: Problem with using topolbuild1_3.tgz

... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110121/8558f18f/attachment-0001.html > > -- > > Message: 4 > Date: Fri, 21 Jan 2011 19:17:47 +0530 > From: Anirban Ghosh > Subject: [gmx-users] CG to FG transformation erro