Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread Justin A. Lemkul
On 7/12/12 9:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Can you please give me an example of such a modeling software? I tried it with PYMOL but the results are not very good. And I also found several programs but the are all not free. http://www.gromacs.org/Documentation/Fil

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread reisingere
Can you please give me an example of such a modeling software? I tried it with PYMOL but the results are not very good. And I also found several programs but the are all not free. Thank you, Eva > > > On 7/12/12 6:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> so you

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread Justin A. Lemkul
On 7/12/12 6:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, so you mean that I first have to add the capping groups to my structure and then run pdb2gmx with the -ter function? Yes. The capping groups (see your force field's .rtp file for available entries) are treat

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread reisingere
Hi Justin, so you mean that I first have to add the capping groups to my structure and then run pdb2gmx with the -ter function? But how can I add the capping groups to the structure? > > > On 7/12/12 4:37 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> I have another question about the

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread Justin A. Lemkul
On 7/12/12 4:37 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I have another question about the option -ter of the pdb2gmx command. I choose it because I thought that this is a way that I can determine what shell happen with the termini but I was not ask anything by the program. My

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread reisingere
I have another question about the option -ter of the pdb2gmx command. I choose it because I thought that this is a way that I can determine what shell happen with the termini but I was not ask anything by the program. My aim is it to block the termini with a neutral group. Is there a way to do th

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-12 Thread reisingere
Hi Justin, thank you for your mail. Sorry that I didn't first check than help. Eva > > > On 7/11/12 10:24 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> >> I wanted to ask if there is a possibility to tell pdb2gmx which residues >> I >> want to be protonated or not. >>

Re: [gmx-users] more than one protonation per residue with pdb2gmx

2012-07-11 Thread Justin A. Lemkul
On 7/11/12 10:24 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I wanted to ask if there is a possibility to tell pdb2gmx which residues I want to be protonated or not. So that I can for example say HIS at position 29 shell be protonated twice. I need this for further e

[gmx-users] more than one protonation per residue with pdb2gmx

2012-07-11 Thread reisingere
Hi everybody, I wanted to ask if there is a possibility to tell pdb2gmx which residues I want to be protonated or not. So that I can for example say HIS at position 29 shell be protonated twice. I need this for further electrostatic analysis. Thank you, Eva -- gmx-users mailing listgmx-use