Re: [gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Justin Lemkul
On 10/2/13 8:45 AM, Andrew Bostick wrote: Dear Justin Thanks for your quick reply. What is reason of this issue? My gro file contains 11383 lines. 11383-3=11380 This value is equal to second line. Sorry, misread your initial post. One of two things is happening: 1. You've used an edit

[gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Andrew Bostick
Dear Justin Thanks for your quick reply. What is reason of this issue? My gro file contains 11383 lines. 11383-3=11380 This value is equal to second line. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at htt

Re: [gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Justin Lemkul
On 10/2/13 8:21 AM, Andrew Bostick wrote: Dear users, I have used grompp command for minimising my system (protein and membrane). I am getting the error: --- Program grompp, VERSION 4.5.1 Source code file: confio.c, line: 744 Fatal error: I

[gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Andrew Bostick
Dear users, I have used grompp command for minimising my system (protein and membrane). I am getting the error: --- Program grompp, VERSION 4.5.1 Source code file: confio.c, line: 744 Fatal error: Invalid line in system.gro for atom 11380: 6

Re: [gmx-users] Invalid line in coordinate file

2012-12-13 Thread Justin Lemkul
On 12/13/12 1:34 AM, Shine Devaraj wrote: Dear users, I have used grompp command for minimising my protein and ligand in membrane after using inflategro command. My system has no problem in visualizing in VMD. The protein is in proper order But I am getting the error ---

[gmx-users] Invalid line in coordinate file

2012-12-12 Thread Shine Devaraj
Dear users, I have used grompp command for minimising my protein and ligand in membrane after using inflategro command. My system has no problem in visualizing in VMD. The protein is in proper order But I am getting the error --- Program grompp, V

Re: [gmx-users] invalid line

2011-04-05 Thread Mark Abraham
On 6/04/2011 4:30 AM, sarah k wrote: dear gromacs users, I'm solvating my protein in nitrogen box. I have changed my spc216.gro, spc.itp and spce.itp files. Don't. In the last 48 hours, I posted a procedure that used genconf to make a box of solvent of a given density. I face the followi

Re: [gmx-users] invalid line

2011-04-05 Thread Justin A. Lemkul
sarah k wrote: dear gromacs users, I'm solvating my protein in nitrogen box. I have changed my spc216.gro, spc.itp and spce.itp files. I face the following error. Changed? In what way? If you're solvating with nitrogen, why are you dealing with water coordinates and topologies? How can

[gmx-users] invalid line

2011-04-05 Thread sarah k
dear gromacs users, I'm solvating my protein in nitrogen box. I have changed my spc216.gro, spc.itp and spce.itp files. I face the following error. How can I fix it? invalid line in /usr/share/gromacs/top/spc216.gro for atom 407: 0.41200 0.41200 0.41200 thanks in advance. Best regards,