[gmx-users] Structure factor reference

Dear gmx users. I asked question about structure factor but I got no reply. I think it's too basic question, Then instead, can any one inform me a good reference paper or book why structure factor must calculate for all atom and not specific types like O-O, O-C, like rdf does? Thank you!! Since

Re: [gmx-users] Variation of box angles - regd

Hi Tsjerk, I am very thankful to you for providing valuable suggestions. Thank you very much. On Tue, Aug 28, 2012 at 9:23 PM, Tsjerk Wassenaar wrote: > Hi Ramesh, > > You can calculate them from the box matrix, or you can let editconf do that > by simply converting the trajectory

Re: [gmx-users] Re: help with "interaction of type atom in the topology"...

On 31/08/2012 1:03 PM, klexa wrote: >> If I recall correctly, the residue number printed by pdb2gmx is actually the residue index (starting from zero), so the problematic residue is MLE, which does have CB. Good thought, but the index here starts counting from 1 (and has done so for at le

[gmx-users] Re: help with "interaction of type atom in the topology"...

>> If I recall correctly, the residue number printed by pdb2gmx is actually the residue index (starting from zero), so the problematic residue is MLE, which does have CB. -Justin Hi Justin, Thank you for the fast response. That makes sense, but the problematic residue is actually both

Re: [gmx-users] Glycoproteion MD

On 8/30/12 9:26 PM, 陈应广 wrote: Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs

Re: [gmx-users] help with "interaction of type atom in the topology database, but an atom of that name was not found in residue" error

On 8/30/12 9:23 PM, Katrina Lexa wrote: Hello Gromacs Users: I apologize for asking a question that has come up several times in the forum, but I have read the answers to those posts and I am not still unable to fix the error based on the suggestions in the previous emails. It

[gmx-users] Glycoproteion MD

Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please s

[gmx-users] help with "interaction of type atom in the topology database, but an atom of that name was not found in residue" error

Hello Gromacs Users: I apologize for asking a question that has come up several times in the forum, but I have read the answers to those posts and I am not still unable to fix the error based on the suggestions in the previous emails. It is completely possible that I am just not seei

Re: [gmx-users] building_insertion_mutants

I've used Macromolecular Builder for inserting loops in proteins. You'll need further minimization and dynamics to get a relaxed structure though, but that's where Gromacs comes in. Erik 30 aug 2012 kl. 18.07 skrev shahid nayeem: > Dear all > I am repeating this mail as it could not get upload

[gmx-users] SangbaeLee: about Gromos forcefield regarding DDM detergent

Dear Gromacs Users. Now we areinterested in GROMACS simulation with PROTEIN + DETERGENT as well as PROTEIN + BILAYER. Could you let me know if you have any information about DETERGENT Gromos force field (especially, we think DDM (n-Dodecyl beta-maltose) is best)? Thanks in advance. Sangbae. =

Re: [gmx-users] Generating insertion mutants

Hi Shahid, You should try homology modeling software, like Modeller. Cheers, Tsjerk On Aug 30, 2012 7:41 AM, "shahid nayeem" wrote: Dear all Please suggest me a tool with which I can generate insertion mutants from a .pdb file. I want to insert new 10-15 aa sequence of AA in between an existi

Re: [gmx-users] generating tripeptides in a box

Hi Pim, I know the problem and also think the problem lies within genbox, but I haven't been able to trace it. A workaround is to solvate with a small box containing a single water moleule. Cheers, Tsjerk On Aug 30, 2012 6:12 PM, "Pim Frederix" wrote: Hello users, I'm experiencing trouble us

[gmx-users] generating tripeptides in a box

Hello users, I'm experiencing trouble using genbox for creating a box of tripeptides in MARTINI CG polarizable water. I feel like any of the options below should do the trick, but all give (different) problems. Generating the randomly place tripeptide box works fine, nothing unusual about the

[gmx-users] building_insertion_mutants

Dear all I am repeating this mail as it could not get uploaded on site. Please suggest me that whether I can insert 15 residue sequence in an existing pdb file and can I get the minimized altered coordinates from here. If not then please suggest an external software or server where I can model this

Re: [gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi

On Thu, Aug 30, 2012 at 1:06 AM, Roland Schulz wrote: > Hi, > > the OpenMM code is still under review. You can download it using I guess you meant OpenMP. As far as I know, the OpenMM build has not been tested much. > git fetch https://gerrit.gromacs.org/gromacs refs/changes/83/1283/14 && git >

Re: [gmx-users] Elastic network model

Hi , Thank you very much .I will take all these factors in to account while building the model. Thank you, Mohan. On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham wrote: > On 30/08/2012 10:17 PM, Mark Abraham wrote: >> >> On 30/08/2012 10:02 PM, mohan maruthi sena wrote: >>> >>> Hi, >>

Re: [gmx-users] Elastic network model

On 30/08/2012 10:17 PM, Mark Abraham wrote: On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in th

Re: [gmx-users] Elastic network model

On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in the change in distance, not harmonic in the di

Re: [gmx-users] Elastic network model

Hi, I am going through it , i will understand it and try to build the topology. Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar wrote: > Hi Mohan, > > You need to check chapter 5 of the gromacs manual to understand the > topology format to write. You probably need onl

Re: [gmx-users] Elastic network model

Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the spe

Re: [gmx-users] Elastic network model

Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have

Re: [gmx-users] Elastic network model

Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to

Re: [gmx-users] do_dssp segmental fault

Hi Deb, I recently installed dssp for Gromacs 4.5.4 on RHEL4 You have to just copy the dsspcmbi downloaded from linux distribution to /usr/local/bin (No need to set an environment variable DSSP if dspcmbi is in /usr/loca/bin as it is the default path for gromacs) Rename the dsspcmbi to dssp chm

[gmx-users] Elastic network model

Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search be

Re: [gmx-users] Charges for Coulomb potential

Alright, I understand now. Many thanks for this! Antoine Le 29/08/2012 18:57, Mark Abraham a écrit : On 30/08/2012 3:18 AM, Delmotte, Antoine wrote: Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 fo