[gmx-users] Re: polymer duplicate atoms

[Dallas Warren]

FYI, I only showed you the bond part of the residue in the previous email (since that was the section I was commenting on and showed how it should be there) there should be some atom details prior to that, as required by the rtp format.  You need to use your own judgment and the manual to ensure it is the correct format for the entry etc.

Plus, you have the atom naming all messed up now.  It is not surprising you are getting an error saying that it can't find atom C1, since the Fbg residue does not have any, you have named it C5.

How have to use the same naming convention as you do with the polymer monomer unit, otherwise you wont be able to automatically cap it.

Another option is to have a Fbg and Fen that includes a capped monomer unit, rather than just the methyl group.  That may be a better way to go about it.

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: Wednesday, 20 March 2013 1:24 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: polymer duplicate atoms
> 
> 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
> successfully
> generate the structure (conf.gro) when I am using pdb2gmx
> command(pdb2gmx
> -ff oplsaa -f 2.pdb -q -missing) with the "-missing" option and
> ignoring the
> hdb file.
> 
> ; rtp file
> [ Fbg ]
>    [ bonds ]
>      C5    +C1
>      C5    H51
>      C5    H52
>      C5    H53
>  [ Fen ]
>    [ bonds ]
>      C6    -C4
>      C6    H11
>      C6    H12
>      C6    H13
> 
> ; hdb file
> Fbg     1
> 3       4       H       C5      +C1     +C2
> Fen     1
> 3       4       H       C6      -C4     -C3
> f2311-differ_residue_num.pdb
> <http://gromacs.5086.n6.nabble.com/file/n5006479/f2311-
> differ_residue_num.pdb>
> 
> 
> 
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-
> tp5006328p5006479.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists