Re: [gmx-users] Atoms in the .top are not numbered consecutively from 1

2012-11-15 Thread Justin Lemkul
On 11/15/12 9:49 AM, Rajiv Gandhi wrote: Hello gmx users, I have created the topology file for my ligand through PRODRG, protein from pdb2gmx. when i try to energy minimize the protein with ligand system it gives error that Atoms in the .top are not numbered consecutively from 1. Could you pl

Re: [gmx-users] Atoms in the .top are not numbered consecutively from 1

2011-06-10 Thread Justin A. Lemkul
sreelakshmi ramesh wrote: Dear all, when i run energy minimization i get the following error. the topology file was created from the starting pdb file using g_x2top *grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3* In general, the use of -maxwarn is discouraged

[gmx-users] Atoms in the .top are not numbered consecutively from 1

2011-06-09 Thread sreelakshmi ramesh
Dear all, when i run energy minimization i get the following error. the topology file was created from the starting pdb file using g_x2top *grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3* Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 348,