RE: AMBER: (no subject)

From: Ross Walker <>
Date: Fri, 30 Jul 2004 09:21:33 -0700

Dear Hayden,

Can you attach the pdb file to an email please so that I can take a look at

> 1. When I load my pdb file into xleap it keeps adding
> countless atoms to the
> system. I have tried using the "protonate" program to correct
> for mismatches

This sounds strange, I suspect that the residue naming and or numbering
inyour pdb file is corrupt in some way. If you can send me the pdb file (or
just the Brookhaven ID will do) I can take a look at it. How much have you
"massaged" the pdb file? Try stripping all of the header (REMARK)
information as well as all the connectivity data. Also go through and make
sure there are TER cards between the different chains. Also, what does the
pdb file look like if you visualise it in vmd for example?

> 2. When I try to create a parm file using saveAmberParm
> <unit> something.parm
> something.crd, it lists all manner of fatal errors.

If the first stage above failed there is no way this section will work so
ignore it for the moment.
> 1. Is there a short and simple way of creating a parm and crd
> file from a pdb
> file? i.e. not necessarily using xleap?

Not that I am aware of. The problem is that the parmtop file needs to
contain parameters for every atom in your system which means that every
residue needs to be identified. If you have unknown residues then you need
to produce parameters for these before you can create the prmtop file. The
prmtop also contains all of the connectivity data which means if can't
successfully identify the residues you can't get the connectivity data
correct. A prmtop file without all this information would be useless for
performing classical simulations. What do you need your prmtop file for? Do
you want it just for visualisation purposes or to run a simulation?

> 2. What is the principal difference in format between AMBER
> pdb files and Brookhaven PDB files.

In terms of what xleap reads in there should be none. All REMARK cards and
connectivity data is ignored. The only issue involves specifying Histidine
protation states (HIP, HID or HIE) and cysteine types (CYS, CYM, CYX). Hence
I think there is probably something wrong with the pdb file you have.

As an aside, do all the tests pass for your Amber installation?

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Jul 30 2004 - 17:53:00 PDT
Custom Search