[gmx-users] specbond recognised but not built

Hi all,   I am using gromacs 3.3.3, and have a specbond definition: CHU C3  2   CHV C4  2   0.2 CHU CHV This is recognised but not built: 7 out of 7 lines of specbond.dat converted successfully Special Atom Distance matrix:     CHU5   

Re: Re[2]: [gmx-users] RE: can gmx be used to simulation NaCl

As I stated in the first sentence, I doubt the usefulness of classical MD for simulating crystallization of NaCl. Whatever I state after that applies to the case of trying it with classical MD nonetheless. Please read closely before trying to outwit however you find on this list. Second, as is

Re: [gmx-users] specbond recognised but not built

Hi Grange, It recognizes the possibility of having a bond between these atoms. That's where the distance matrix comes in. But if a bond were made, you'd have a statement right after the distance matrix saying something like linking atom ... and atom It doesn't happen, and the reason is the

Re: [gmx-users] specbond recognised but not built

Thankyou very much Tsjerk, indeed this was the problem. I am most relieved this was the solution. I had assumed the distance was an upper bound on the acceptable distance. - Original Message From: Tsjerk Wassenaar [EMAIL PROTECTED] To: Discussion list for GROMACS users

[gmx-users] specbond # bonds

Hi, does the following specbond.dat line build a double bond between the two atoms?  CHU    C3      2      CHV    C4      2      0.2    CHU    CHV What would happen if the first number was 2 but the second number was 1 ? Would two C4s need to be at the right distance away from the one C3? Thanks,  

Re: [gmx-users] specbond # bonds

I suggest consulting the wiki: http://wiki.gromacs.org/index.php/specbond.dat -Justin Grange Hermitage wrote: Hi, does the following specbond.dat line build a double bond between the two atoms? CHUC3 2 CHVC4 2 0.2CHUCHV What would happen if the first

[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position restrain? 1.we will keep position restrain on all the

Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

minnale wrote: HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position restrain? 1.we will keep position restrain on

[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position restrain? 1.we will keep position restrain on all the

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water, is there any possibility to move water inside pore of the membrane when keep restrain only on protein. Could you please tell me Thanks a lot in advance On

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water, is there any possibility to move water inside pore of the membrane when keep restrain only on protein. Could you please tell me Thanks a lot in advance On

Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

minnale wrote: Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water, is there any possibility to move water inside pore of the membrane when keep restrain only on protein. Could you please tell me Thanks a

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

Thanks for your invaluable reply to Justin and syma. On Sun, 29 Jun 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water, is there any possibility to move

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

Hi, If the position restraints are only on the protein, then the water and lipids are free to move about- assuming you have a cavity in your protein wide enough to accommodate water- then water (or lipids) depending on the nature and location of the cavity, should move in as a vacuum is not

[gmx-users] AFM Pulling index.ndx pull.ppa

Hello, I am attempting to use AFM pulling on a 17 amino acid peptide, but am having trouble with the 'group' concept. I've read the manual and searched sample XXX.ndx files, but have had no luck. How would I define the first amino acid as the reference group (i.e. - fixed in space) and the last

[gmx-users] tpbconv functionality

I found the tpbconv tool very usefull for generating tpr files for resuming the simulations. Nevertheless I couldn't find an option to set/change the number of processors to use as the -np option in grompp. Is there a way to do this? ___ gmx-users

[gmx-users] Re: warning mesgs

HI, When I use the merge command along with pdb2gmx to form inter disulphide bonds between two different chains, its removing a water molecule to connect the two ends. Its like forming a peptide bond which I dont wish. Is there any way to tell to gromacs, to create the inter dishulphide bonds

Re: [gmx-users] ff53b6 for GROMACS 3.3.X?

Thanks for your response Berk. I have never heard of GROMOS 53b6. Does it exist? Yes it does. I have a pdf with parameters for GROMOS 53A6 and GROMOS 53B6 (vacuo). After attempting to locate the source it appears to be distributed to us (the pdf) when someone from Zurich was visiting.

[gmx-users] anyone knows how to install grace?

Hi I want to use grace 5.1.9 (normally xmvgr). each time i do installation using ./configure, it prompts motif not found . So i tried to find free softare openmotif (it can do the same work as motif). Having successfully installed openmotif , the grace installation , however, still tells me