?
Thaankks! :)
Sincerely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Monday, July 9, 2012 12:35 AM
Subject: Re: [gmx-users] define a new residue
On 7/8/12 12:43 PM, Shima Arasteh wrote:
> OK.
> What about generating an outpu
;)
Anyway, thanks!
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Monday, July 9, 2012 12:35 AM
Subject: Re: [gmx-users] define a new residue
On 7/8/12 12:43 PM, Shima Arasteh wrote:
> OK.
> What about generat
On 7/8/12 12:43 PM, Shima Arasteh wrote:
OK.
What about generating an output file through CGenFF by the first 3 residues of
the protein, rather thn the first 2 (formyl+valine)?
Maybe. Try it and see, rather than waiting a few hours for someone to get
around to replying :)
-Justin
--
=
9:02 PM
Subject: Re: [gmx-users] define a new residue
On 7/8/12 11:29 AM, Shima Arasteh wrote:
> Thanks all.
> So if I find a protein which is parametrized by CHARMM and then find the
> valine residue there, I might use the parameters of side chains of it in my
> own rtp
On 7/8/12 11:29 AM, Shima Arasteh wrote:
Thanks all.
So if I find a protein which is parametrized by CHARMM and then find the valine
residue there, I might use the parameters of side chains of it in my own rtp
file. Right?
You can look this up in the force field's .rtp file. For full par
for GROMACS users
Cc: Shima Arasteh
Sent: Sunday, July 8, 2012 4:44 PM
Subject: Re: [gmx-users] define a new residue
Usually in CHARMM the sidechains are parametrized as separate blocks and than
merged to the backbone.
In fact backbone, in charmm aminoacids, have always tha same charges
u need a better parameterization protocol using a more suitable
model compound.
-Justin
Sincerely,
Shima
From: francesco oteri
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Sunday, July 8, 2012 3:28 PM
Subject: Re: [gmx-users] define a new residue
012 3:28 PM
Subject: Re: [gmx-users] define a new residue
Why have you removed the hydrogen?
2012/7/8 Shima Arasteh
Dear Francesco,
>Thanks. Honestly I thought about this, but I don't know how much charges I
>need to increase or decrease of other atoms?
>
>Is it possible to a
m.
Thanks for your suggestions.
Cheers,
Shima
From: francesco oteri
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Sunday, July 8, 2012 3:04 PM
Subject: Re: [gmx-users] define a new residue
Hi Shima,
usually charge calculation are carried out on
Hi dear gmx friends,
I got the parameters of formyl-valine through the CHARMM website. Now I need to
define it as a new residue FVAL( as Justin suggested me earlier) in .rtp file.
To set the correct charges for atoms, I used the CHARMM output. In order to
define FVAL to rtp file, I added these
Thank you so much.
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Saturday, April 14, 2012 9:28 PM
Subject: Re: [gmx-users] Define a new residue in oplsaa
Shima Arasteh wrote:
> Dear Justin,
> Thank you so much.
>
:* Justin A. Lemkul
*To:* Shima Arasteh ; Discussion list for
GROMACS users
*Sent:* Saturday, April 14, 2012 9:19 PM
*Subject:* Re: [gmx-users] Define a new residue in oplsaa
Shima Arasteh wrote:
> Dear GROMACS users,
> I wanna add add a FOR residue containing atom C and O. In oplsaa
force
Shima Arasteh wrote:
Dear GROMACS users,
I wanna add add a FOR residue containing atom C and O. In oplsaa force
field, the most similar residue to formyl (FOR) is ACE.
How I can change the ACE in .rtp file in oplsaa ff to define FOR residue
as a new residue?
I did like this, Is it correct?
Dear GROMACS users,
I wanna add add a FOR residue containing atom C and O. In oplsaa force field,
the most similar residue to formyl (FOR) is ACE.
How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a
new residue?
I did like this, Is it correct?
[ ACE ]
[ atoms ]
CH3
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