[gmx-users] pdb2gmx fatal error

2012-11-09 Thread Marco Gerolin
Hello, I know that is an already know problem but I don't know how to move on. running pdb2gmx I had this message Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 163. Residue 163 is a GLY and has no a

Re: [gmx-users] pdb2gmx-fatal error in output file

2010-05-09 Thread Mark Abraham
On 10/05/2010 1:49 AM, Justin A. Lemkul wrote: Moeed wrote: Hello, output.pdb2gmx is giving Fatal error: Fatal error: Residue '' not found in residue topology database. Do I need to add Hexane topology to rtp file in library?! Please see below. Thank you very much. It looks

Re: [gmx-users] pdb2gmx-fatal error in output file

2010-05-09 Thread Justin A. Lemkul
Moeed wrote: Hello, output.pdb2gmx is giving Fatal error: Fatal error: Residue '' not found in residue topology database. Do I need to add Hexane topology to rtp file in library?! Please see below. Thank you very much. It looks like the format of your .pdb file is wrong. p

[gmx-users] pdb2gmx-fatal error in output file

2010-05-09 Thread Moeed
Hello, output.pdb2gmx is giving Fatal error: Fatal error: Residue '' not found in residue topology database. Do I need to add Hexane topology to rtp file in library?! Please see below. Thank you very much. ***

Re: [gmx-users] pdb2gmx fatal error

2009-06-26 Thread Justin A. Lemkul
Dave Hassan wrote: Hi, I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt. When I run pdb2gmx with the G43a1 force field I get the error: Warning: 'DG' not found in residue topology database, trying to use 'DGUA' --- Pro

[gmx-users] pdb2gmx fatal error

2009-06-26 Thread Dave Hassan
Hi, I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt. When I run pdb2gmx with the G43a1 force field I get the error: Warning: 'DG' not found in residue topology database, trying to use 'DGUA' --- Program pdb2gmx, VERSION 4