Re: [gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

2007-11-30 Thread David van der Spoel
himanshu khandelia wrote: Sorry, there was a little mistake in the reported output of grompp in my previous email. It should be as follows: ## Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) Warning: atom names in protein.top and final.gro don't match

Re: [gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

2007-11-30 Thread Justin A. Lemkul
Your procedure sounds like it could induce an error in a number of steps. Have you considered simply submitting your initial .pdb file to a program like Sybyl or DeepView and allowing it to make the mutation for you? -Justin Quoting himanshu khandelia <[EMAIL PROTECTED]>: > Sorry, there was a

[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

2007-11-30 Thread himanshu khandelia
Sorry, there was a little mistake in the reported output of grompp in my previous email. It should be as follows: ## Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) Warning: atom names in protein.top and final.gro don't match (CE1 - CD2) Warning: atom n