[gmx-users] Re: polymer duplicate atoms

[Dallas Warren]

As noted by your rtp entry:

>   [ bonds ]
>     C1    -C4
>     C1    H11
>     C1    H12
>     C1    C2
>     C2    F21
>     C2    F22
>     C2    +C3
>     C3    F31
>     C3    F32
>     C3    C4
>     C4    F4
>     C4    Cl4
>     C4    +C1

One end of the residue bonds via the C1 to a C4 in the next residue, and the other end of the residue bonds via the C4 to a C1 in the next residue.

Your beginning and ends to your polymer have to show this, which they currently do not.  The rtp entry for both of them do not say anything about how they bond to the next residue.  It should be more something like this ...

 [ Fbg ]
   [ bonds ]
     C4    +C1
     C4    H11
     C4    H12
     C4    H13

 [ Fen ]

   [ bonds ]
     C1    -C4
     C1    H11
     C1    H12
     C1    H13

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of cqgzc
> Sent: Tuesday, 19 March 2013 12:50 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
> 
> 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 ]
>     C1    opls_135           -0.568    1
>     H11   opls_140            0.274    1
>     H12   opls_140            0.273    1
>     C2    opls_962            0.373    2
>     F21   opls_965           -0.165    2
>     F22   opls_965           -0.159    2
>     C3    opls_962            0.182    3
>     F31   opls_965           -0.133    3
>     F32   opls_965           -0.144    3
>     C4    opls_963            0.142    4
>     F4    opls_965           -0.142    4
>     Cl4   opls_151            0.066    4
>   [ bonds ]
>     C1    -C4
>     C1    H11
>     C1    H12
>     C1    C2
>     C2    F21
>     C2    F22
>     C2    +C3
>     C3    F31
>     C3    F32
>     C3    C4
>     C4    F4
>     C4    Cl4
>     C4    +C1
> 
> ; Terminal f2311 residue ("beginning" of chain)
> ; designation arbitrary, C1 is -CH3
> [ Fbg ]
>   [ atoms ]
>     C1    opls_135           -0.565     1
>     H11   opls_140            0.198     1
>     H12   opls_140            0.208     1
>     H13   opls_140            0.209     1
>   [ bonds ]
>     C1    H11
>     C1    H12
>     C1    H13
> ; Terminal f2311 residue ("end" of chain)
> ; designation arbitrary, C1 is -CH3
> [ Fen ]
>   [ atoms ]
>     C1    opls_135           -0.705    1
>     H11   opls_140            0.248    1
>     H12   opls_140            0.246    1
>     H13   opls_140            0.245    1
>   [ bonds ]
>     C1    H11
>     C1    H12
>     C1    H13
> 
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-
> tp5006328p5006428.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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