Re: [gmx-users] A common error Atom O11 in residue bDM 1 was

2010-09-26 Thread Justin A. Lemkul
ABEL Stephane 175950 wrote: You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem happens ? Should I change the name of these atoms in the rtp and pdb files ? Is a trick is available to avoid this "bad" translation ? The only option i

[gmx-users] A common error Atom O11 in residue bDM 1 was

2010-09-26 Thread ABEL Stephane 175950
You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem happens ? Should I change the name of these atoms in the rtp and pdb files ? Is a trick is available to avoid this "bad" translation ? Stefane ABEL Stephane 175950 wrote: > Dear a

Re: [gmx-users] A common error Atom O11 in residue bDM 1 was not found in rtp entry

2010-09-25 Thread Justin A. Lemkul
ABEL Stephane 175950 wrote: Dear all, I have a very "common" problem when I try to convert a pdb file to a gro file with the following command. I use charmm27ff and gmx4.5.1. pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp I obtain the following "commun" error : "Atom O1

[gmx-users] A common error Atom O11 in residue bDM 1 was not found in rtp entry

2010-09-25 Thread ABEL Stephane 175950
Dear all, I have a very "common" problem when I try to convert a pdb file to a gro file with the following command. I use charmm27ff and gmx4.5.1. pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp I obtain the following "commun" error : "Atom O11 in residue bDM 1 was not fou