Re: [gmx-users] g_sas vdwradii.dat

On 31/12/2011 5:04 PM, afsaneh maleki wrote: Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, when I did simulation. It seem that it use the default value of 0.12 nm. W

[gmx-users] g_sas vdwradii.dat

Hi, I finished the simulation of a peptide in DOPC bilayer in according to tutorial by Dr. Justin. I had not added van der Waals radius of phosphorous in the vdwradii.dat file, when I did simulation. It seem that it use the default value of 0.12 nm. When I use g_sas command, I get the following wa

Re: [gmx-users] g_sas Vdwradii.dat

maite lopez cabezas wrote: Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité

Re: [gmx-users] g_sas Vdwradii.dat

Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité On Sat, Jun 7, 2008 at 4:50 PM, Dav

Re: [gmx-users] g_sas Vdwradii.dat

Xavier Periole wrote: On Sat, 07 Jun 2008 22:32:29 +0200 "Xavier Periole" <[EMAIL PROTECTED]> wrote: On Sat, 7 Jun 2008 15:04:34 -0400 "maite lopez cabezas" <[EMAIL PROTECTED]> wrote: Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a V

Re: [gmx-users] g_sas Vdwradii.dat

On Sat, 07 Jun 2008 22:32:29 +0200 "Xavier Periole" <[EMAIL PROTECTED]> wrote: On Sat, 7 Jun 2008 15:04:34 -0400 "maite lopez cabezas" <[EMAIL PROTECTED]> wrote: Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a Van der Waals radius for 1

Re: [gmx-users] g_sas Vdwradii.dat

On Sat, 7 Jun 2008 15:04:34 -0400 "maite lopez cabezas" <[EMAIL PROTECTED]> wrote: Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a Van der Waals radius for 128 atoms 3840 out of 6400 atoms were classified as hydrophobic I saw that the **

[gmx-users] g_sas Vdwradii.dat

Hi: I'm using g_sas *to analyse a DPPC simulation but it gave the next warning: WARNING: could not find a Van der Waals radius for 128 atoms 3840 out of 6400 atoms were classified as hydrophobic I saw that the **Van der Waals radius for phophorous atoms doesn't appear in vdwraddi.dat. When I modif