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
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
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>
> On 7/12/12 6:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>> so you
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
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?
>
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> On 7/12/12 4:37 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> I have another question about the
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
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
Hi Justin,
thank you for your mail.
Sorry that I didn't first check than help.
Eva
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> 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.
>>
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
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
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