aipo...@gmail.com
<mailto:saipo...@gmail.com>>>> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>
<mailto:saipo...@gmail.com
<mailto:saipo...@gma
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>
ail.com
<mailto:saipo...@gmail.com>>> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>
<mailto:saipo...@gmail.com
u choosing as your termini when running
>>pdb2gmx? It
>> should be "none," since by capping, you are not choosing a
>> protonation state for the N- and C-termini.
>>
>> -Justin
>>
>&g
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com <mailto:saipo...@gmail.com>>>>
What are you choosing as your termini when running pdb2gmx? It
>>should be "none," since by capping, you are not choosing a
>>protonation state for the N- and C-termini.
>>
>>-Justin
>>
>>
>> Pooja
>>
>>
aipo...@gmail.com>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>,
Discussion lis
;> "none," since by capping, you are not choosing a protonation state for the
>> N- and C-termini.
>>
>> -Justin
>>
>>
>>> Pooja
>>>
>>>
>>>
>>> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
>>> >> mark.
by capping, you are not choosing a protonation state for the
> N- and C-termini.
>
> -Justin
>
>
>> Pooja
>>
>>
>>
>> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>
>>
&g
lto:mark.abra...@anu.edu.au>> wrote:
- Original Message -
From: Sai Pooja mailto:saipo...@gmail.com>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for
GROMACS use
aminoacids.n.tdb file as well?
Pooja
On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Friday, July 2, 2010 7:28
> Subject: Re: [gmx-users] Capping residues
> To: jalem...@vt.edu, Discussion list for GROMACS users <
- Original Message -
From: Sai Pooja
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping residues
To: jalem...@vt.edu, Discussion list for GROMACS users
> I am sorry if I did not frame the question correctly, but putting it very
> simply, is there a way to use c
I am sorry if I did not frame the question correctly, but putting it very
simply, is there a way to use capping residues with the charmm forcefield if
the residues are --COCH3 and NHCH3?
On Thu, Jul 1, 2010 at 4:58 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Would it be possible to a
Sai Pooja wrote:
Would it be possible to add some capping residues (like --COCH3 and
--NHCH3) by writing a separate .itp file and including it in the
topology file? Is there a way to make it consistent with charmm forcefield?
No, because you have to specify bonds between these capping resi
must one do before using these .rtp files?
On Wed, Jun 30, 2010 at 8:39 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: "Justin A. Lemkul"
> Date: Thursday, July 1, 2010 9:58
> Subject: Re: [gmx-users] Capping residues
> To: Discussion list for G
- Original Message -
From: "Justin A. Lemkul"
Date: Thursday, July 1, 2010 9:58
Subject: Re: [gmx-users] Capping residues
To: Discussion list for GROMACS users
>
>
> Sai Pooja wrote:
> >Hi,
> >
> >1) What capping residues are recognized by ch
Sai Pooja wrote:
Hi,
1) What capping residues are recognized by charmm implemented on gromacs
in the latest git version?
It looks like there aren't any. Check the .rtp file to be sure.
I was trying to use ACE for acetyl but it is not recognized by pdb2gmx.
2) Is it possible to define c
Hi,
1) What capping residues are recognized by charmm implemented on gromacs in
the latest git version?
I was trying to use ACE for acetyl but it is not recognized by pdb2gmx.
2) Is it possible to define caps at residues other than those at the
termini?
Regards
Pooja
--
Quaerendo Invenietis-S
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