GROMACS users
Sent: Monday, May 14, 2012 12:42 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 14/05/2012 6:00 PM, Shima Arasteh wrote:
Thanks for your suggestions.
>Now, I think that it's better to add the N atom of next residue to the .pdb
&
:42 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 14/05/2012 6:00 PM, Shima Arasteh wrote:
Thanks for your suggestions.
>Now, I think that it's better to add the N atom of next residue to the .pdb
>file and then add hydrogen atoms to its .
;
> [ dihedrals ]
> O C +N +CA
> H C +N +H
>
There are other possible dihedrals here.
-Justin
>
>
>
> *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
> *To:* Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>
>
ely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sunday, May 13, 2012 9:40 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/13/12 12:42 PM, Shima Arasteh wrote:
> OK, so I entered the H atom cor
---
*From:* Justin A. Lemkul
*To:* Discussion list for GROMACS users
*Sent:* Sunday, May 13, 2012 9:44 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/13/12 1:06 PM, Shima Arasteh wrote:
> Even in gromos87, if I want to make a .rtp file for
for GROMACS users
> *Sent:* Sunday, May 13, 2012 8:36 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
>
>
>
> On 5/13/12 11:43 AM, Shima Arasteh wrote:
> > Again thanks for all your replies.
> > As I got through yo
Thanks,
It was just a question and I prefer to use the CHARMM36.
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sunday, May 13, 2012 9:44 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5
Lemkul mailto:jalem...@vt.edu>>
> *To:* Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
> *Sent:* Saturday, May 12, 2012 10:12 PM
> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
residue pairs
>
>
>
> On 5/12/12 1:37 P
---
*From:* Justin A. Lemkul
*To:* Discussion list for GROMACS users
*Sent:* Sunday, May 13, 2012 8:36 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/13/12 11:43 AM, Shima Arasteh wrote:
> Again thanks for all your replies.
> As I got through
t for GROMACS users
Sent: Sunday, May 13, 2012 8:36 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/13/12 11:43 AM, Shima Arasteh wrote:
> Again thanks for all your replies.
> As I got through your advices, I found that the atoms contribut
:36 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/13/12 11:43 AM, Shima Arasteh wrote:
> Again thanks for all your replies.
> As I got through your advices, I found that the atoms contribute in making
> bonds
> and angles in a resid
Shima
*From:* Justin A. Lemkul
*To:* Discussion list for GROMACS users
*Sent:* Saturday, May 12, 2012 10:12 PM
*Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/12/12 1:37 PM, Justin A. L
which I can get through the files of
swissparam?
Thanks in advance, and sorry for disturbing you friends.
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Saturday, May 12, 2012 10:12 PM
Subject: Re: [gmx-users] Fatal error: No atoms
All right.
Thank you
Sincerely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Saturday, May 12, 2012 10:36 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/12/12 2:00 PM, Shima
line ?:
[ dihedrals ]
O C +N CA
Cheers,
Shima
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Saturday, May 12, 2012 10:07 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/12/12 2:00 PM, Shima Arasteh wrote:
The total charge is zero in real but what I got through swissparam is as below:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 C=O 1 LIG C 1 0.4500 12.0110
2 O=C 1 LIG O 2 -0.5700 15.9994
3 HCMM 1 LIG H1 3 0.0600 1.0079
4 HCMM 1 LIG H2 4 0.0600
+N CA
Cheers,
Shima
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Saturday, May 12, 2012 10:07 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/12/12 1:32 PM, Shima
On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
On 5/12/12 1:32 PM, Shima Arasteh wrote:
Dear gmx users,
I want to simulate a peptide in water. The peptide has a formyl residue as the
N-terminus. I got the parameters of it and then add it to the .rtp file of
charmm36.ff as below:
[ For ]
[ ato
On 5/12/12 1:32 PM, Shima Arasteh wrote:
Dear gmx users,
I want to simulate a peptide in water. The peptide has a formyl residue as the
N-terminus. I got the parameters of it and then add it to the .rtp file of
charmm36.ff as below:
[ For ]
[ atoms ]
; name type charge chargegroup
C C 0.4500
Dear gmx users,
I want to simulate a peptide in water. The peptide has a formyl residue as the
N-terminus. I got the parameters of it and then add it to the .rtp file of
charmm36.ff as below:
[ For ]
[ atoms ]
; name type charge chargegroup
C C 0.4500 0
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