[gmx-users] merge ligand and protein

Dear All   I tried to merge the ligand togethere with the protein by using pdb2gmx. However, it doesn't work. Is there another way to merge ligand and protein together.   Thank you so much for all of the answers Best RegardKanin ___ gmx-users mail

Re: [gmx-users] merge ligand and protein

On Tuesday 12 September 2006 10:00, kanin wichapong wrote: > Dear All >I tried to merge the ligand togethere with the protein by using > pdb2gmx. However, it doesn't work. Is there another way to merge ligand and > protein together. >Thank you so much for all of the answers take a

Re: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

Una, In your case you can also try the T-coupling groups Protein and Non-Protein, without providing a .ndx file. However, in general give some thoughts to temperature coupling (groups) when setting up your system and try to grasp how groups are treated in gromacs. Hope it helps, Tsjerk On 9/11

[gmx-users] merger ligand and protein to constriant

Hi all  I already look in the turorial however that is not the thing that I try to look for. I would like to merge the ligand into the protein and then make the contrain between two atoms, one from the liagand and one from the protein. However, as far as I know, I can do the constraint or restraint

Re:[gmx-users] merger ligand and protein to constriant

What about merging the ligand the the protein by DeepView? In your mail: >From: "kanin wichapong" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: gmx-users@gromacs.org >Subject: [gmx-users] merger ligand and protein to constriant >Date:Tue, 12 Sep 2006 13:40:59 +0200 > >H

Re: [gmx-users] merger ligand and protein to constriant

Hi, you can also have different chains (Protein and Ligand) and constrain them. Using the -merge option you can merge the ligand into the protein but for that you need the topology for the ligand (as rtf, not from prodrg). If you use Prodrg-topology you first set up the protein without ligand.

[gmx-users] cross terms!!

hello,gmx-users yes! thanks david!! where and how the cross terms, like bond-bond and bond-angle cross potential terms, designated in the parameter file. the mannual had these potential functions but i don't know how to switch it off, so as to make the parameter for my sy

Re: [gmx-users] cross terms!!

Rongliang Wu wrote: hello,gmx-users yes! thanks david!! where and how the cross terms, like bond-bond and bond-angle cross potential terms, designated in the parameter file. the mannual had these potential functions but i don't know how to switch it off, so as to make t

[gmx-users] RB dihedral potential query in OPLS

hello gmx users, First of all thanks to Chris for his response to my previous mail.But I still have a doubt regarding RB potential which I would like to get clarified about. I would be very thankfull if you can go through my post (patiently) and comment on it. _

[gmx-users] re: RB dihedral potential query in OPLS

Those OPLS-AA "Ryckaert Bellemans" terms are intended to work with [ pairs ]. They are not the same as the real RB terms. Here is a good explaination: http://www.gromacs.org/pipermail/gmx-users/2004-May/010500.html "The original Ryckaert Bellemans potential is for carbon tails only (e.g. decane,

[gmx-users] CVS password

Hi, I executed this command : cvs -z3 -d :ext:@cvs.gromacs.org:/home/gmx/cvs co gmx But I don't have the password. What is the password? Thanks. ALVARO FERNANDEZ ``` GRUPO DE QUÍMICA TEÓRICA: /\\ PROCESOS DINÁMICOS EN QUÍMICA |()||

[gmx-users] Fatal error: Force field inconsistency

Hello, I had this error while trying to run a simulation for a small molecule without water and bilayer, I have included in the topol.top its parameters taken from OPLS and its topology, since I did not created the topology with the pdb2gmx I did not included the ffoplsa.itp in the topol, howeve

[gmx-users] running CPMD with GROMACS interface in SGI irix 6.5

Hi   I got some trouble in running CPMD with GROMACS interface in SGI irix 6.5. Thanks in advance   the error is  [PEAK NUMBER  116]   PEAK MEMORY  14169180 =  113.4 MBytes [ALL. NUMBER  116]  TOTAL MEMORY  13983696 =  111.9 MBytes =

[gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.

Hello, I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, the periodic parameters of dihedral angles have been converted into Ryckaert-Bellemans ones. I have tried to find more info about this in the CHARMM and Gromacs documentations but I have not found much. Why exactly th

[gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters

Hello, I'm trying to use an implementation of the CHARMM force fields in Gromacs and I'm still a little bit confused about how Gromacs retrieves the bonded/non-bonded parameters when the .top file is created. Concretely, I have : 1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameter

Re: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.

> Hello, > > I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, > the periodic parameters of dihedral angles have been converted into > Ryckaert-Bellemans ones. I have tried to find more info about this in the > CHARMM and Gromacs documentations but I have not found much. Why

Re: [gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters

> Hello, > > I'm trying to use an implementation of the CHARMM force fields in Gromacs > and I'm still a little bit confused about how Gromacs retrieves the > bonded/non-bonded parameters when the .top file is created. Concretely, > I have : > 1. a ffcharmmnb.itp where I have defined specific 1-4

[gmx-users] A method to scale Coulombic 1-4 interactions seperately

There is a recent publication about combining the Berger lipids with OPLS-AA and getting the correct 1-4 scaling factor. New dihedrals were developed because it is possible to set special 1-4 parameters for LJ, but not coulomb. However, there is another workaround to this that should be generally a

[gmx-users] wham question

hi all does anyone have an example/tutorial of how to do umbrella sampling using gromacs & wham? i'm about to try to calculate free energies of binding using this method. i can find no information whatsoever about 'wham.gct', which is an optional input mentioned in the mdrun online reference pag

Re: [gmx-users] Re: Simulation problem with extended membrane system!

If I solvate my GPCR into the DPPC128 system using genbox, there are only about 50 lipids left, which I think are too few, so I want a larger starting structure.According to your note, when I did step 3, loaded my DPPC183 system to VMD, I found the edges lined up poorly, there is are gaps between t

[gmx-users] Re: Simulation problem with extended membrane system!

>If I solvate my GPCR into the DPPC128 system using genbox, there are only >about 50 lipids left, which I think are too few, so I want a larger starting >structure. >According to your note, when I did step 3, loaded my DPPC183 system to VMD, >I found the edges lined up poorly, there is are gaps be

[gmx-users] how to write a annealing .mdp

hello everyone   i want to anneal my system,but i don't konw how to wrote a right annealing-mdp! could anyone give me a moldel?   tanks in advaced!               3G 时 代 来 临 了，坚 决 对 传 统 邮 箱 说 不 ！ 新 一 代 极 速 3G 邮 箱 闪 亮 登 场 ，280 兆 网 盘 免 费 送 ！ 点 击 此 处 注 册

[gmx-users] does the conformation cause this error?

hi all i have a problem:when i did the mdrun ,it stopped early for error:Maximum force =  9.0996275e+09 on atom 606 Norm of force =  2.8519283e+08    does this cause by the conformation?and how to resolve it?     3G 时 代 来 临 了，坚 决

Re: [gmx-users] does the conformation cause this error?

zzhwise1 wrote: > hi all > i have a problem:when i did the mdrun ,it stopped early for > error:Maximum force = 9.0996275e+09 on atom 606 > Norm of force = 2.8519283e+08 > > does this cause by the conformation?and how to reso