[gmx-users] Output of rotation

2012-09-30 Thread Shima Arasteh
Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to generate a topology file of it, GROMACS asks for terminals one by one, ( 2 N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are lost and the total charge is incorrect. The pdb

Re: [gmx-users] on tpbconv

2012-09-30 Thread rama david
Yes it will work .. Just at the time of mdrun add -cpi cpt ( prvious cpt file ) With best wishes and regards..!! On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, for my original MD, based on mdp file the total time is 500 ps. After it finished, I have

Re: [gmx-users] Output of rotation

2012-09-30 Thread Tsjerk Wassenaar
Hi Shima, How did you rotate the structure? Probably the TER records got lost in the process. Cheers, Tsjerk On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, I have .pdb file. This .pdb file represents a dimer protein. When I try to

Re: [gmx-users] Output of rotation

2012-09-30 Thread Shima Arasteh
The input file has TER  between 2 monomers. The command which I use is: #editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro After that, I use editconf to convert .gro to .pdb file: #editconf -f protein-rotate.gro -o protein.pdb The residue numbers after 10th one of output pdb

Re: [gmx-users] Calculate Density with respect to time...

2012-09-30 Thread rama david
Thank you for your immediate reply.. I need the xvg graph that will tell me the density of water in between the protein with respect to time . g_densmap not give such out put.. Sol please would you tell me how to do it ??? How to select the Sol that are only in between the protein ?? Thank

Re: [gmx-users] .itp and .rtp file modifications?

2012-09-30 Thread Justin Lemkul
On 9/29/12 11:47 PM, Elie M wrote: Dear all, I am trying to minimize the energy of a polymer system I have. I have successfully modified the n2t file to include force fields for atoms that were not present. However now I am using grompp before using mdrun (to minimize). However I have a

Re: [gmx-users] number of coordinates in coordinate file does not match topology -reg

2012-09-30 Thread Justin Lemkul
On 9/30/12 1:06 PM, venkatesh s wrote: Respected gromacs users now iam buliding the simulation system for protein + peptide simulation (manually insert the peptide into the protein structure file after the TER ) following commands i used here 1. pdb2gmx -f

[gmx-users] Re: g_wham

2012-09-30 Thread Justin Lemkul
Please keep all Gromacs-related correspondence on the gmx-users mailing list. I am CC'ing this message there and would ask that all further correspondence be posted to the list so that you can benefit from commentary from the entire community. See comments below. On 9/30/12 2:09 PM, Chris

[gmx-users] Error with grompp

2012-09-30 Thread Elie M
Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called ffoplsaamod.n2t. The top file was created successfully. However when I run grompp, I get the

[gmx-users] DNA orientation restraint

2012-09-30 Thread 仝督读
Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX

[gmx-users] DNA orientation restrain

2012-09-30 Thread 仝督读
Hi everyone, I am doing a DNA simulation in a long simulation box (the lengthen of z is much larger than x and y). So I want to constrain the DNA molecule lying along the z axis. But I don't know how to realize this in GROMACS. Actually I notice there is orientation restraints in 4.3.5 of GMX