Re: [gmx-users] Regarding error

On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana wrote: > Respected Sir, > > While i am running the gromacs software to simulate > the protein i am getting the following error. > > Fatal error: > Residue 'GNP' not found in residue topology database > > http://www.gromac

[gmx-users] Regarding error

Respected Sir, While i am running the gromacs software to simulate the protein i am getting the following error. Fatal error: Residue 'GNP' not found in residue topology database Suryanarayna Seera, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

On 30/04/2012 3:38 PM, Anirban Ghosh wrote: On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung mailto:adeyo...@andrew.cmu.edu>> wrote: Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to star

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung wrote: > Hi, > > Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you > know, automatic threading is awesome because it allows me to start parallel > runs without calling mpirun. So on version 4.5.5, I can start a job on > eight

RE: [gmx-users] Error in using gromacs for MD simulation

I have posted this to the gromacs users emailing list. No files came through, generally they are stripped off the emails before being posted to the emailing list. Should never send attachments to an emailing list, post them to the internet and put the URLs in the email for people to look at if

[gmx-users] RE: ask about SDF

I have sent this email to the gromacs users emailing list. I don't actually use g_spatial as it doesn't do what I want it to, I use the older g_sdf script. So can't comment on the output or really help you with it. What you are doing seems right from a quick look through. From what you have t

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

> Does the cylinder geometry work if you use "pull_start = no" and pull_init1 > equal to your starting (restraint) distance? I'm just trying to go through > all > of the iterations of what might be failing. In theory, what you're doing is > fine but I'd be interested to know if there was som

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

On 4/29/12 4:46 AM, J B wrote: > Is the problem specific to cylinder geometry? Do other settings work? Does it > make a difference if you set values for pull_r0 and pull_r1? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull = umbrella pull

Re: [gmx-users] Make an index file

Dear Mark, Wow, That was kind of you. I appreciate you. Ok, I will try it. Thanks,Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Sunday, April 29, 2012 2:11 PM Subject: Re: [gmx-users] Make an index file On 29/04/2012 7:32 PM, Shima Ar

Re: [gmx-users] disulfide bonds

thank you very much That was what I've tried to use "pdb2gmx-ss", this is not useful, 'cause it's not in the same unit. My problem is not the distance. Hagit 2012/4/29, Mark Abraham : > On 29/04/2012 7:02 PM, Hagit G wrote: >> I'm trying to work on thrombin pdf file with 2 chains. The pdb co

Re: [gmx-users] Make an index file

Dear MArkWow, That was kind of you. I appreciate you. Ok, I will try it. Thanks, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Sunday, April 29, 2012 2:11 PM Subject: Re: [gmx-users] Make an index file On 29/04/2012 7:32 PM, Shima Ar

Re: [gmx-users] Make an index file

On 29/04/2012 7:32 PM, Shima Arasteh wrote: Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title= NVT equilibration for POPC define= -DPOSRES; position restra

Re: [gmx-users] Make an index file

Actually, I am confused somehow. I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below. title        = NVT equilibration for POPC define        = -DPOSRES    ; position restrain the protein ; Run parameters integrator   

Re: [gmx-users] disulfide bonds

On 29/04/2012 7:02 PM, Hagit G wrote: I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atom

[gmx-users] disulfide bonds

I'm trying to work on thrombin pdf file with 2 chains. The pdb code is 1PPB.pdb The main problem is: When I use pdb2gmx it adds H atoms to Cys, hence the disulfide bonds are no longer conected after energy minimization. How can I avoid this addition of H atoms? (I tried to make this bond after, but

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

> Is the problem specific to cylinder geometry? Do other settings work? Does > it > make a difference if you set values for pull_r0 and pull_r1? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull= umbrellapull_geometry