AMBER Archive (2006)

Subject: RE: AMBER: antechamber problem

From: Baker, Bo-Yang (BakerBY_at_peds.ucsf.edu)
Date: Mon Jan 02 2006 - 18:23:40 CST

Dear Ilyas

Thank you very much for your detailed intructions. Now I am getting understand what was wrong with my ligand pdb file. I load the chol5.pdb that is adapted from your attachment, and generate a chol5.prep and chol5.parm file. Then use 'xleap' to load the n62ch5.pdb, that is adapted from your attachment. It went through without any fatal error this time, such as:

>FATAL: Atom .R<HIE 163>.A<HD1 18> does not have a type.

Cheers!

All the best! Happy New Year

Bo

 

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Ilyas Yildirim
Sent: Fri 12/30/2005 4:25 PM
To: amber_at_scripps.edu
Cc:
Subject: Re: AMBER: antechamber problem
> But, I notice that in the pdb file, atoms start from "C", then end with
> "H". But in the .prep file, each "C" atom is followed by their "H". I use
> 'antechamber' (Amber7) to generate the .prep file from the choleterol pdb
> file. I try the "babel" to generate a new "chol3a.pdb" from the oringinal
> chol.pdb, but it is the same order as before: start with "C', then edn
> with "H". I have attached the files. I am not sure this is the cause for
> the problem in "tleap". It may be worth to fix this part first. Or I have
> to mannually change all the atom type of ligand in the .pdb file? Is
> there easy way to name the atoms in pdb file in order to match with that
> in the .prep file?

Dear Bo,

Sorry for the late response. I checked out your files, and here are my
comments:

First, create your .pdb file for 'chol' molecule, and then create the
.prep file using antechamber. In your chol3.pdb file, u have to have
unique atom names. Check out the file I have attached (chol3_new.pdb).

Then use antechamber to create the .prep file. Here, it is important what
kind of a charge method you are using. As an example;

antechamber -i chol3_new.pdb -fi pdb -o chol3_new.prepi -fo prepi -c bcc
-nc 0 -at gaff

will use the bcc charge method, and the gaff atom types. If you have the
charges for each atom in the 'chol' molecule in a file, u can give that
file explicitely, too, using antechamber.

Then, copy/paste the 'chol' molecule (which has the 'UNK' residue name)
into your n62ch1c.pdb file (check out n62ch1c_new.pdb). Also, use the
'TER' card in your .pdb file to divide the seperate structures.

Now, everything is almost ready. Then create an xleap.in file as the
following:

----------------------- xleap.in -------------------------------
source leaprc.ff99
source leaprc.gaff
loadamberparams chol3.parm
loadamberprep chol3_new.prep
molecule = loadpdb n62ch1c_new.pdb
----------------------------------------------------------------

Here, the leaprc.ff99 is going to have the 'capital' lettered atom type
parameters while leaprc.gaff has the 'lower' lettered atom type
parameters. Your system, 'n62ch1c', is described using both of these force
field paramaters; namely ff99 and gaff (antechamber with 'gaff' creates
'lower' lettered atom types for the atoms). When u load these into xleap,
u will see that it will add 5 atoms to the loaded .pdb file.

Now, check your molecule using the 'check molecule' in xleap. There will
be some error messages and warnings. Warnings are generally showing the
close contact informations, which arent that important right now. U can
get rid of them by minimizing the structure. The error messages are the
ones you have to give care. As an example, I am getting the following
error message:

FATAL: Atom .R<HIE 163>.A<HD1 18> does not have a type.

The HD1 atom on HIE (originally it was a HIS residue, but I dont know why
leap has changed it to HIE) does not have an atom type. If you check out
the messages in xleap, u will see that xleap has added 5 H atoms to the
structure. Checking out the HIE aminoacid, I dont see an atom named as
'HD1'. That means that in your original .pdb file, the atoms named as
'HD1' in the HIS residues are not correctly named. U have to change those
names to the names used in 'xleap' (or simply just deleted those atoms in
your original .pdb file, and let xleap add them for you).

After doing that, load the new .pdb file to xleap. Check the structure
again, and hopefully u wont have any error messages. The charge of the
structure should be an integer, keep that in mind.

Hope this helps. Good luck.

Ilyas

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