Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Thanks. Summary: 1) *.gro from pdb2gmx has no chain id information 2) pdb2gmx has an option to output pdb file 3) If you want to make groups based on chain id : pdb2gmx -ignh -ff ${forcefield} -f input.pdb -o a.pdb make_ndx -f a.pdb -o a.ndx > a.output.make_ndx 4) mdrun has an o

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: *.gro has no chain id information. I can not make energy group(based on chain id) from *.gro file generated by pdb2gmx See the mail I just sent. 3. Don't strip H, just to add them back again :) I have the structure minimized.pdb after EM. minimized.pdb is

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: I tried to make energy groups from the "output" (*.gro) from pdb2gmx. > Found 0 atoms with chain identifier B Group is empty > Found 0 atoms with chain identifier A Group is empty That means no chain id information in *.gro, but I have to define the energy groups a

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

On Wed, Jan 28, 2009 at 6:32 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> Hi, >> >> Thank for your helpful reply. >> >> I understand your feeling. If you have time, please see the following. >> >> mdrun has an option to output the final structure(-c). I just knew it >> after read

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Hi, On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham wrote: > Liu Shiyong wrote: > >> Hi, >> > > >> *Step 2:* >> Starting structure: clean2.pdb >> >> I am trying to calculate the energy according to energy groups >> >> >> pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i >> clean2_0.6.posre.

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: Hi, Thank for your helpful reply. I understand your feeling. If you have time, please see the following. mdrun has an option to output the final structure(-c). I just knew it after reading your post and checked again :< Thanks . Firstly, I run a minimized com

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: Hi, *Step 2:* Starting structure: clean2.pdb I am trying to calculate the energy according to energy groups pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i clean2_0.6.posre.itp -o clean2_0.6.gro > clean2_0.6.output.pdb2gmx 2>&1 make_ndx -f clean2.pdb -o clean

Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Hi, Thank for your helpful reply. I understand your feeling. If you have time, please see the following. mdrun has an option to output the final structure(-c). I just knew it after reading your post and checked again :< Thanks . Firstly, I run a minimized command to get the minimized

Re: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: Hi, Did you get my script ? As I said just a few days ago, I don't run jobs for people. I only have allocated time on our University's cluster, which I need for myself. That said, it is also very difficult to go through someone's scripting, laden with variables that

Re: [gmx-users] Invalid atom number 6415 in indexfile

Hi, Did you get my script ? I dump a frame from .trr file. I did not define xtc-grps On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> Hi, >> >> I got an error when do grompp: The input PDB file comes from the output >> of GROMACS by trajconv command. >>

Re: [gmx-users] Invalid atom number 6415 in indexfile

Liu Shiyong wrote: Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command. --- Program grompp, VERSION 3.3.3 Source code file: ../../../../src/kernel/readir.c, line: 838 *Fatal e

[gmx-users] Invalid atom number 6415 in indexfile

Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command. *Here is the log from grompp:* Option Filename Type Description -f em.mdp Input, Opt! grompp input