Re: [gmx-users] genbox using TIP3P?
WILLIAM R WELCH wrote: Hello I would like to use the TIP3P model in my calculation, and I would like to be able to use genbox to solvate a pepetide, but there is no TIP3P.gro coordinate file in the program. I there such a coordinate file available? Any 3-point water model will be fine for generating solvent coordinates - the standard practice in GROMACS is to solvate with spc216.gro (per man genbox) and then in the .top file to #include "tip3p.itp" Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] fitting procedure in g_rmsf
[EMAIL PROTECTED] wrote: Hello, I have a rather basic query. I want to know which atoms of the reference structure will be used for fitting , in g_rmsf program. In the program g_rms there are separate options for fitting and calcualation of rmsd. I wonder if it is possible for the user to select a set of atoms for fitting and calculate the rmsf over another range of atoms or the whole protein, similar as in g_rms program. Probably. In fact, I'd be amazed if the same functionality were not present in g_rmsf as in g_rms, not that I've used the former. Have you tried it out to see? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using TIP3P?--Nevermind
Nevermind, I made one using VMD, it solvated my protien just fine. - Original Message - From: WILLIAM R WELCH <[EMAIL PROTECTED]> Date: Friday, February 2, 2007 3:25 pm Subject: [gmx-users] genbox using TIP3P? To: Discussion list for GROMACS users > Hello > I would like to use the TIP3P model in my calculation, and I would > like to be able to use genbox to solvate a pepetide, but there is no > TIP3P.gro coordinate file in the program. I there such a coordinate > file available? > Will > > - Original Message - > From: [EMAIL PROTECTED] > Date: Friday, February 2, 2007 11:46 am > Subject: [gmx-users] fitting procedure in g_rmsf > To: gmx-users@gromacs.org > > > > Hello, > > > > I have a rather basic query. > > I want to know which atoms of the reference structure will be used > for > > fitting , in g_rmsf program. > > In the program g_rms there are separate options for fitting and > > calcualation of rmsd. I wonder if it is possible for the user to > > select a > > set of atoms for fitting and calculate the rmsf over another range > of > > atoms or the whole protein, similar as in g_rms program. > > > > Waiting for your suggessions. > > > > sridhar > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox using TIP3P?
Hello I would like to use the TIP3P model in my calculation, and I would like to be able to use genbox to solvate a pepetide, but there is no TIP3P.gro coordinate file in the program. I there such a coordinate file available? Will - Original Message - From: [EMAIL PROTECTED] Date: Friday, February 2, 2007 11:46 am Subject: [gmx-users] fitting procedure in g_rmsf To: gmx-users@gromacs.org > Hello, > > I have a rather basic query. > I want to know which atoms of the reference structure will be used for > fitting , in g_rmsf program. > In the program g_rms there are separate options for fitting and > calcualation of rmsd. I wonder if it is possible for the user to > select a > set of atoms for fitting and calculate the rmsf over another range of > atoms or the whole protein, similar as in g_rms program. > > Waiting for your suggessions. > > sridhar > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fitting procedure in g_rmsf
Hello, I have a rather basic query. I want to know which atoms of the reference structure will be used for fitting , in g_rmsf program. In the program g_rms there are separate options for fitting and calcualation of rmsd. I wonder if it is possible for the user to select a set of atoms for fitting and calculate the rmsf over another range of atoms or the whole protein, similar as in g_rms program. Waiting for your suggessions. sridhar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox peptide-membrane simulation
Maite, The option -d sets a distance to be met on all sides, considering all the atoms to in the ouput selection. That's not what you want for a membrane now, is it? So, you don't want that option. You should have a box from the lipids anyway, I guess (used to equilibrate that system), just extend the z-coordinate (third number in the last row of the .gro file) such that your peptide fits in. Furthermore, molecules can't go out of the box, there is no outside! There's only wrapping from one side to the opposite one. Please read the manual and the mailing list regarding periodic boundary conditions (and setting up membrane-peptide simulations). Tsjerk On 2/2/07, maite lopez <[EMAIL PROTECTED]> wrote: Hi gromacs users: I'm simulating a peptide-dppc64 system. When i create my box with editconf program (editconf -f input.gro -o output.gro -bt triclinic -c -d 1.5) and i solvate, the molecule go out of the box. I used many kind of box and some box sizes. My system size is 4.936 4.408 and 10.503 nm. Should i use -d option with editconf? I've found in the gmx-users list and in many tutorials, it should be no less than 0.5. I don't want to solvate the system in x and y axes due to the interaction betwen lipids and water. I did it whit editconf -f input.gro -o output.gro -bt triclinic -c -box 4.936 4.408 12 , but i didn't use the -d option. Is that ok? So my question is: Can I do something whit -d and -box option of editconf program for resulting in a system that it doesn't solvate in x and y axes, and the molecule isn't out? I need to solvate in z axes. whould you please help me? best regard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than 5 digits of the number of atoms and residue
On Feb 2, 2007, at 8:42 AM, David van der Spoel wrote: Cherry Y. Yates wrote: Dear GROMACS users and developers, In the .gro files, there are only 5 digits reserved for the atom number and residue number. But if I have more than 1 million atoms or residues, may I just increase the column number from 5 to 6? I guess not, then how to simulate such system? you can use g96 files instead. ...or just restart the numbering of residues or atoms from 1 when you hit the column width. This is particularly useful for PDB files, if you want to visualize a large system in PyMOL/VMD. Cheers, ERik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
