AMBER Archive (2009)

Subject: Re: [AMBER] Ligand covalent bonds appear to be broken

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Fri Oct 30 2009 - 06:53:44 CDT

If I'm not mistaken, ptraj doesn't write bond information to PDBs. So
VMD has to guess where the bonds are based on atom names and distances
between atoms. In some cases bonds in your ligand exceed the canonical
bond lengths, so VMD doesn't draw the bond. The prmtop files, on the
other hand, have explicit bond information so VMD doesn't have to
guess.

--Tom

2009/10/30 <moitrayee_at_mbu.iisc.ernet.in>:
> Dear Amber Users,
>
> I am facing a problem when visualizing my simulations with VMD. I am following
> two methods:
>
> 1. I convert my crds to pdbs using ptraj. The script for it using the following
> actions:
>
> rms first out rms @CA
> center @CA
> image
> strip :WAT
>
> go
>
>
> When I load this pdbs to VMD using animatepdbs.tcl script (available at VMD site
> to load multiple pdbs), everything seems allright except my ligand, in which
> some covalent bonds appear to be broken for the line or bond representation of
> the ligand. However, using VDW sphere representation, I can see the whole ligand
> intact.
>
> 2. I use another method for visualization. I directly load my trajectories to
> VMD using the parameter files and crds. In this case, I find no such error.
> Everything is perfectly fine in all representation types.
>
> Is this some visualisation effect ? Please help me with your valuable
> suggestions/comments.
>
> Thanks a lot in advance.
>
> Best Regards,
> Moitrayee
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber