Re: [gmx-users] Residue 'UNK' not found in residue topology database

On 9/19/12 8:31 AM, naga sundar wrote: Dear simone I think so u r using the same pr.mdp and md.mdp files what u created initially. So open both the mdp files replace DRG with UNK and the try sure it will work out. The error is from pdb2gmx, so .mdp alterations will have

Re: [gmx-users] Residue 'UNK' not found in residue topology database

Dear simone I think so u r using the same pr.mdp and md.mdp files what u created initially. So open both the mdp files replace DRG with UNK and the try sure it will work out. On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul wrote: > > > On 9/18/12 12:42 PM, SIMONE BROGI wrote:

Re: [gmx-users] Residue 'UNK' not found in residue topology database

On 9/18/12 12:42 PM, SIMONE BROGI wrote: Dear gromacs user, I have a complex generated by docking calculation and I would perform a MD by gromacs. I have a problem with ligand atoms. In the pdb file the ligand appears as UNK and if I process this file in order to start simulation I receive this

[gmx-users] Residue 'UNK' not found in residue topology database

Dear gromacs user, I have a complex generated by docking calculation and I would perform a MD by gromacs. I have a problem with ligand atoms. In the pdb file the ligand appears as UNK and if I process this file in order to start simulation I receive this messagge error: "Residue 'UNK' not found in

RE: [gmx-users] Residue 'UNK' not found in residue topology database

See: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_ residue_topology_database Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTE

Re: [gmx-users] Residue 'UNK' not found in residue topology database

Sagittarius wrote: Dear Gromacs users, Could you please help me to find out what the problem is. Curiously enough, pdb2gmx is telling you want the problem is. I use command pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top Fatal error: Residue 'UNK' not

Re: [gmx-users] Residue 'UNK' not found in residue topology database

Sorry, but first I suggest: Read the error message! Fatal error: > Residue 'UNK' not found in residue topology database Now, what could this mean? This actually means, in the forcefield residue database (e.g. ffoplsaa.rtp) exists no entry for a molecule named UNK... Rename the pdb to the expec

[gmx-users] Residue 'UNK' not found in residue topology database

Dear Gromacs users, Could you please help me to find out what the problem is. I use command pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top formaldehyde.pdb looks like this: COMPNDUNNAMED