Re: [gmx-users] constraint distance between ligand and protein

2006-09-13 Thread David Mobley
Kanin, On 9/11/06, kanin wichapong <[EMAIL PROTECTED]> wrote: Hi All, I would like to know how to make a distance constraint between the ligand and the protein. If I just merge two chain together by pdb2gmx, it can done if the two chain are both protein. However, if it is a ligand and protei

Re: Re: SV: Re: [gmx-users] constraint distance

2006-09-13 Thread David Mobley
Allow me to take this opportunity to reiterate that the ability to only apply distance/angle/dihedral restraints between atoms in the same "molecule" (in the topology sense) is really lame. It would be really nice if GROMACS could handle absolute atom numbering for restraints (i.e. using the numbe

SV: Re: SV: Re: [gmx-users] constraint distance

2006-09-11 Thread Soren Enemark
David van der Spoel <[EMAIL PROTECTED]> skrev: Soren Enemark wrote:> Hi,> maybe I am misunderstanding either the manual or the topic.. but - in > my world -> I never stop being puzzled by the part of chapt 6 in the manual which > apparently> says that such distance constraining is possible even

Re: SV: Re: [gmx-users] constraint distance

2006-09-11 Thread Mark Abraham
> Hi, > maybe I am misunderstanding either the manual or the topic.. but - in my > world - > I never stop being puzzled by the part of chapt 6 in the manual which > apparently > says that such distance constraining is possible even though it (seems) > to be > secretly known that it is _not

Re: SV: Re: [gmx-users] constraint distance

2006-09-11 Thread David van der Spoel
Soren Enemark wrote: Hi, maybe I am misunderstanding either the manual or the topic.. but - in my world - I never stop being puzzled by the part of chapt 6 in the manual which apparently says that such distance constraining is possible even though it (seems) to be secretly known that it i

SV: Re: [gmx-users] constraint distance

2006-09-11 Thread Soren Enemark
 Hi,  maybe I am misunderstanding either the manual or the topic.. but - in my world -  I never stop being puzzled by the part of chapt 6 in the manual which apparently  says that such distance constraining is possible even though it (seems) to be  secretly known that it is _not_ possible unless on

Re: [gmx-users] constraint distance

2006-09-11 Thread Tsjerk Wassenaar
Hi Kanin, The only way to get away with that is to merge your two parts to form one molecule, with the only connection being a distance_restraint (or another bonded term if you want to emulate bond-like behaviour such as a salt-bridge). Best, Tsjerk On 9/11/06, kanin wichapong <[EMAIL PROTECTE