Hi,
Thank you again for your suggestions. The way I generate my structure
is by lattice method and the structure was without any relaxation.
I have modified the structure and used only one molecule (26 atom the
way you suggested to me). It is relaxed now but still I am facing the
same problem regarding the connectivity. The structure looks fine in
VMD. I am attaching the pdb file with this mail can you please suggest
what is wrong in this? Any suggestion is appreciated.
Thank you in advance!
Regards,
Sanket
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
Date: Thursday, November 8, 2007 8:28 pm
Subject: Re: AMBER: Amber 9: Generating Input files for EVB simulations
of the crosslinked structures (Hydrogels)
To: amber.scripps.edu
> On Thu, Nov 08, 2007, sanket deshmukh wrote:
>
> > Thanks for your suggestions David. I created a pdb file without any
> > united atom in it (attaching it with this email) but still I am
> facing> the same problem. Antechamber can't find the connectivity
> properly.
> Two points:
>
> 1. Antechamber on works on single residues, not on entire chains
> or sets of
> chains.
>
> 2. You pdb file has lines like these:
>
> ATOM 1 C3 GLY 1 6.000 12.000 10.000
> ATOM 2 C3 GLY 1 5.000 13.000 11.000
> ATOM 3 C GLY 1 5.000 11.000 9.000
> ATOM 4 O GLY 1 6.000 12.000 8.000
> ATOM 5 OS GLY 1 4.000 12.000 8.000
> ATOM 6 C3 GLY 1 3.000 11.000 9.000
> ATOM 7 C3 GLY 1 5.000 13.000 9.000
> ATOM 8 OS GLY 1 4.000 14.000 10.000
>
> First, the coordinates look like garbage. Second, atom names
> within a residue
> must have unique names, and you have several atoms in GLY 1 named
> "C3".Third, since what you are calling GLY clearly isn't glycine,
> Amber will most
> likely get confused: don't call something GLY that is not glycine.
>
> I could go on (e.g. you have another GLY residue (starting at atom
> 212) that
> contains only hydrogens and nothing else). You need to "start
> small", and
> make sure you understand how antehcamber works with a minimal
> molecule, then
> think about building up more complex systems.
>
> And, use a molecular viewer (say, VMD or Chimera) to visualize your
> pdb file
> before sending it to antechamber: this will certainly help avoiding
> obviousflaws in the pdb file.
>
> ...dac
>
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
- application/octet-stream attachment: hyd.pdb
Received on Sun Nov 25 2007 - 06:07:44 PST
