: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Wednesday, 20 March 2013 1:24 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
>
> I follow your advice to edit the bond conditions of residues F
I follow your advice to edit the bond conditions of residues Fbg and Fen in
my rtp file. Subsequently, I should modify the hdb file to add hydrogens for
Fbg and Fen. However, I get the fatal error message " Atom +C1 not found in
residue Fbg 113, rtp entry Fbg while adding hydrogens." I can successf
rs-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Tuesday, 19 March 2013 12:50 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
>
> I have successfully construct the polymer chain of length 1 using the
>
I have successfully construct the polymer chain of length 1 using the OPLS
force field. The rtp file as follow:
; F2311 - this is an internal residue
[ Fre ]
[ atoms ]
C1opls_135 -0.5681
H11 opls_1400.2741
H12 opls_1400.2731
C
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Monday, 18 March 2013 12:54 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
>
> I want to construct a polymer chain of F2311 with 112 length. In my pdb
> file,
> residues Fre, Fbg and Fen denote
I want to construct a polymer chain of F2311 with 112 length. In my pdb file,
residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)—
,terminate part (Fbg:the beginning of chain with methyl; Fen: the end of
chain with methyl), respectively. It looks like CH3-A-B...
A-B-A-B-A-B...-A-B
I want to construct a polymer chain of F2311 with 112 length. In my pdb file,
residues Fre, Fbg and Fen denote the repeat unit —(CH2-CF2-CF2-CFCl)—
,terminate part (Fbg:the beginning of chain with methyl; Fen: the end of
chain with methyl), respectively. It looks like CH3-A-B...
A-B-A-B-A-B...-A-B
mer, every problem begins to resemble a
nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of cqgzc
> Sent: Friday, 15 March 2013 6:20 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: polymer dupl
Dear Dallas
Thanks for your reply. I followed the way of you said to modify the
residue number in sequence. It generated a complete sturctural file
(conf.gro) without deleting the duplicate atoms. However, it denoted another
strange structure which contained many seperated residue
—(CH2-C
Dear Dallas
Thanks for your reply. I followed the way of you said to modify the
residue number in sequence. It generated a complete sturctural file
(conf.gro) without deleting the duplicate atoms. However, it denoted another
strange structure which contained many seperated residue
—(CH2-CF
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