[gmx-users] All-atom MD simulation of a protein at 323K and 283K

I am trying to compare the stability of a protein from two organisms which live in the aforesaid temperature. I am wondering it would make sense to run MD simulation in gromacs with Amber99sb in these temperature since force field parameterization was carried out in room temperature. I am

[gmx-users] Problem with g_hbond perl script output

Hi GMX-users, I have been having issues with plot_hbmap.pl because the output it included has none of the residues I am suggesting it to find. I get my hbmap.xpm file by using g_hbond and picking the ligand group first only to receive this output after running perl: # DonorAcceptor %

Re: [gmx-users] All-atom MD simulation of a protein at 323K and 283K

Hi, What you need to be aware of is that heat capacities aren't well reflected by the force field, hence the temperature offset from 300 K may not be well reflected either. As such, your simulation at 323 K may in fact be more representative of let's say 335 K or something. I can't comment on

Re: [gmx-users] All-atom MD simulation of a protein at 323K and 283K

On 5/8/14, 2:48 AM, Pappu Kumar wrote: I am trying to compare the stability of a protein from two organisms which live in the aforesaid temperature. I am wondering it would make sense to run MD simulation in gromacs with Amber99sb in these temperature since force field parameterization was

Re: [gmx-users] Problem with g_hbond perl script output

On 5/8/14, 5:14 AM, Jacob Babinec wrote: Hi GMX-users, I have been having issues with plot_hbmap.pl because the output it included has none of the residues I am suggesting it to find. I get my hbmap.xpm file by using g_hbond and picking the ligand group first only to receive this output

Re: [gmx-users] query regarding automated topology builder and repository

On 5/8/14, 1:06 AM, Sanchaita Rajkhowa wrote: Dear all, I would like to know if automated topology builder and repository server http://compbio.biosci.uq.edu.au/atb/index.py?tab=existing_tabnocache=836 gives the correct topology for ligands? For e.g. I have to build topology for

[gmx-users] Protein preparation in Membrane simulation

Dear all When doing membrane simulation, do protein needs to be prepared in Xleap module in Amber as given in tutorials (Bevans Lab). regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Degree of hydrogen bonding

Thank you Justin for quick reply. I did exactly what you have mentioned but the thing is I am getting number of hydrogen bonds per monomer higher than what i was expecting. Is it possible to see which polymer atom have the hydrogen bond.( I mean is there a way to see specific atoms using the

Re: [gmx-users] Degree of hydrogen bonding

On 5/8/14, 11:21 AM, Udaya Dahal wrote: Thank you Justin for quick reply. I did exactly what you have mentioned but the thing is I am getting number of hydrogen bonds per monomer higher than what i was expecting. Is it possible to see which polymer atom have the hydrogen bond.( I mean is

Re: [gmx-users] Degree of hydrogen bonding

Hi, Check out g_hbond -h... documentation is written for a reason ;-) You sound like you want to see the existence matrix. You might want to create some index groups for small parts of your polymer, unless you want to drown while interpreting -hbn and -hbm. Mark On Thu, May 8, 2014 at 5:21 PM,

Re: [gmx-users] npt dynamics generate a lot of pdb files

By modifying nstlist, you're very likely fixing a symptom, rather than fixing the problem. Mark On Thu, May 8, 2014 at 6:21 PM, Natalia Alveal F. nalv...@bio.puc.clwrote: Dear Gromacs users, Reducing the nstlist value works for me. Thanks a lot for yours suggestions. 2014-05-06 22:47

[gmx-users] RMSD

Dear gromacs users Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] force field

Dear friends who knows about force field choosing in zinc ion complex with amyloid beta peptide protein??? i,m looking forward to your reply thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

Dear all, I'm trying to determine the binding energy of a membrane protein to the membrane. Ultimately I need to compare the binding energy of the same protein to two similar types of lipid, the hypothesis being that there should be a slight difference. I considered two options: alchemical

Re: [gmx-users] force field

On 5/8/14, 2:48 PM, elham tazikeh wrote: Dear friends who knows about force field choosing in zinc ion complex with amyloid beta peptide protein??? What does you survey of the literature suggest? The force field choice is one of, if not the single most important choices you will make in

Re: [gmx-users] Binding energy of membrane protein to the membrane lipids

On 5/8/14, 3:38 PM, Victor Sojo wrote: Dear all, I'm trying to determine the binding energy of a membrane protein to the membrane. Ultimately I need to compare the binding energy of the same protein to two similar types of lipid, the hypothesis being that there should be a slight difference.

[gmx-users] Does anyone use GROMACS for carbohydrates?

Hello all, I am looking to use GROMACS to simulate carbohydrate-protein systems, and I'm interested in hearing if anyone has any experience with this, or if there any cautions or caveats I should be aware of. Best, Tamir Dingjan -- Gromacs Users mailing list * Please search the archive at

[gmx-users] force field

Dear Justin thanks for your quick reply i,mgoing to simulate zinc ion on Amyloid beta peptide at 300k...and i choose 1ZE9 as pdb my choice is correct or i have to pdb of protein without cation for my work or can i delete zinc ion effect in that pdb? for force field choosing ,i think Opls is