AMBER Archive (2007)

Subject: RE: AMBER: convert pdb files to restart files

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jan 16 2007 - 09:19:54 CST

> is there anyway that AMBER could convert pdb files to
> restart files without having to use the tleap
> program?
>
> i have thousands of pdb files and it would be nice to
> have a command like ambpdb.

No not really. If they are all identical topology you could create the one
prmtop file and write your own script to simply write coordinates in the
correct format.

However, you might as well simply use tleap in script mode. This is real
easy. You can create a txt file containing the instructions you want tleap
to carry out. E.g.

source leaprc.ff99SB
mymol = loadpdb molecule1.pdb
solvatebox mymol TIP3PBOX 10.0
saveamberparm mymol molecule1.prmtop molecule1.inpcrd
quit

Then you execute tleap as:

tleap -s -f script.x

It is then a simple matter to write a shell script that loops over all your
pdb files, creates a script.x with the correct pdb filename, calls tleap,
then creates a new script.x for the next pdb etc etc.

In this way you don't have to enter any commands interactively.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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