AMBER Archive (2006)

Subject: AMBER: VMD PDB into LEAP Readable PDB

From: Akshay Patny (
Date: Wed Oct 04 2006 - 20:07:11 CDT

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

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

I look forward to hear from you.

Kind Regards
Akshay Patny
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