Re: [gmx-users] pdb2gmx not recognizing disulfides

Russell Green wrote: I did try changing the bond length but it wouldn't catch all the disulfides. I do have multiple chains but I don't believe they should be merged. My current work around is to just leave the disulfide residues named CYX according to the amber format and then change them

Re: [gmx-users] pdb2gmx not recognizing disulfides

>I did try changing the bond length but it wouldn't catch all the > disulfides. I do have multiple chains but I don't believe they should be > merged. My current work around is to just leave the disulfide residues > named > CYX according to the amber format and then change them to CYS2 in the .

Re: [gmx-users] translate

mahbubeh zarrabi wrote: Dear all i want to translate the protein coordinates to center of the hole in membrane(i want to insert protein in membrane).how can i do it with editconf. thanks editconf -h

Re: [gmx-users] Gromacs Performance mesurement

> Friends; > > > > Is there any tool/ procedure available to measure/calculate Gromacs > performance on a AMD Opetron (Single processor 64-bit) m/c ? > > Any pointer to determine the above will be helpful. Did you look at the gromacs webpage, where the front page has a link to "benchmarks"? Mark

Re: [gmx-users] pdb2gmx not recognizing disulfides

I did try changing the bond length but it wouldn't catch all the disulfides. I do have multiple chains but I don't believe they should be merged. My current work around is to just leave the disulfide residues named CYX according to the amber format and then change them to CYS2 in the .itp files

[gmx-users] Gromacs Performance mesurement

Friends; Is there any tool/ procedure available to measure/calculate Gromacs performance on a AMD Opetron (Single processor 64-bit) m/c ? Any pointer to determine the above will be helpful. Thank You; URPradhan At Gmail Dot Com ___ gmx-user

Re: [gmx-users] pdb2gmx not recognizing disulfides

Hi Russel, You never mentioned the distance between the 'sulphurs-that-wouldn't-connect'. Are they beyond the range normal for disulphide bonds? If so, you could try to add an additional entry in the specbond.dat file with a different bond length. Maybe you'll have to change the residue name firs

Re: [gmx-users] [Fwd: How simulate two peptides in a box?]

Hi Fufeng Liu, I guess you ran pdb2gmx on the two peptides, where both peptides had the same chain identifiers. In that case, pdb2gmx will assume that it's one molecule and connect them. Use chain identifiers to indicate the different peptides, or build topologies first on separate files and comb

[gmx-users] translate

Dear all i want to translate the protein coordinates to center of the hole in membrane(i want to insert protein in membrane).how can i do it with editconf. thanks Looking for a deal? Find great prices on

Re: [gmx-users] pdb2gmx not recognizing disulfides

Russell Green wrote: Hello, I just changed the disulfide max bond length in the specbond.dat file to various numbers (0.4, 0.5, 1.2, 8.0, ...) and pdb2gmx only assigns some of the disulfides in my protein but not all. If I use 0.4, it finds 22 of the 52 CYS residues to be in disulfide bonds w

Re: [gmx-users] pdb2gmx not recognizing disulfides

Hello, I just changed the disulfide max bond length in the specbond.dat file to various numbers (0.4, 0.5, 1.2, 8.0, ...) and pdb2gmx only assigns some of the disulfides in my protein but not all. If I use 0.4, it finds 22 of the 52 CYS residues to be in disulfide bonds when all 52 should be in d

[gmx-users] [Fwd: How simulate two peptides in a box?]

Please keep requests for help on the list. That way they're archived for others to use, and other people can raise points of interest. The last sentence here http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off is my suggestion for you :-) Probably, you have only one [molecu

Re: [gmx-users] pdb2gmx not recognizing disulfides

> Hello, > > I'm having problems with pdb2gmx not recognizing disulfides in my > protein. I've tried chaning the residue name and -ss flag but neither > works. > I read that this was a known bug on the website. Does anyone have a fix > for > this? Did you use specbond.dat correctly? http://wik

Re: [gmx-users] pdb2gmx not recognizing disulfides

Russell Green wrote: Hello, I'm having problems with pdb2gmx not recognizing disulfides in my protein. I've tried chaning the residue name and -ss flag but neither works. I read that this was a known bug on the website. Does anyone have a fix for this? please submit a bugzilla if there

Re: [gmx-users] center of mass

> Dear all > i want to determine the center of mass of my protein > in the z-dimension.which command in gromacs is useful > for me? Did you look in section 7.3.12 of the manual? Demonstrating a credible attempt to solve your own problem is much more likely to generate useful answers for you. Peopl

Re: [gmx-users] How to proceed with energy minimization for Normal Mode Analysis

> Hi, > I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. > For that I require a well minimized structure. I have minimized my > structure using steepest descent and conjugate gradient. But the structure > seems to have got struct in a local energy minima. How should I proce