VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 06 2006 - 14:59:36 CDT

Hi,
  I'm no Amber expert, but if you can identify what needs to
be done to your atom and residue names, I can assist you with
writing the scripts to truncate or rename your atoms to please
LEAP. You might ask on the Amber mailing list what the restrictions
are and the best suggested change for your files, and once you find out,
we can write a script to automate the process. It would be nice to
make it easy to do things like this if this problem is a common one
for Amber users.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 04, 2006 at 08:09:14PM -0500, Akshay Patny wrote:
> Dear Amber Users
>
> I have generated a GPCR protein system embedded in membrane
> using the VMD scripts. The system now has:
> 1. Protein 2. POPC bilayer 3. Water 4. Chloride Ions
>
> Finally I have the PDB and corresponding PSF files of the
> entire system consisting of roughly 40,000 atoms.
>
> I intend to do the MD simulation in Amber8/9. Now the
> problem is that this PDB file is not in a format which is
> readable by LEAP properly.
>
> Some of the problems which i have identified include:
>
> 1. The names of some heavy atoms are 4 characters long e.g.
> C321. I guess this is not allowed as the max characters
> allowed are 3 except for hydrogens which can have 4.
>
> 2. The residue names have 4 characters and these should be 3
> for LEAP.
>
> 3. Thw water residues are present as TIP3, these need to be
> changed to WAT to be recognized as TIP3 water in the LEAP
>
> 4. Is chain information required?
>
> There were a number of errors when i tried to load this file
> into the LEAP.
>
> Is there a neat way (some script) to convert this VMD PDB
> file in a way so that it becomes readable by LEAP properly?
> or else is the entire file has to be edited manually to make
> corrections??
>
> I know people have created their intial membrane-protein
> system using VMD and later simulated using AMBER. I woould
> appreciate if you can suggest me how to do the same
> properly.
>
> I look forward to hear from you.
>
> Kind Regards
> Akshay Patny 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078