AMBER Archive (2008)

Subject: Re: AMBER: using packmol file in Amber

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Fri Dec 05 2008 - 09:49:39 CST

        
        
        
        
        

1
from a pdb file, create a gaussin input using antechamber:

antechamber
-i n-octane.pdb -fi pdb -o octane_gin.gjf -fo gcrt

2
Run the gaussian

3
antechamber -i octane_gin.out -fi gout -o octane.gaff.prep -fo prepi
-nc 0 -c resp -rn OAS

4
parmchk -i octane.gaff. prep -f prepi -o octane.frcmod

5
antechamber -i octane.gaff.prep -fi prepi -o octane.gaff.pdb -fo pdb

6
use packmol with octane.gaff.pdb for getting 1 molecule ( as you
suggested ) octane1.packmol.pdb file

7
xleap -s -f leaprc.gaff

8
octane = loadpdb octane.gaff.pdb

9
saveoff octane octane.lib

10
Quit

11
xleap -s -f leaprc.gaff

12
loadoff octane.lib

13
loadamberparams octane.frcmod

14
 OCS = octane1.packmol.pdb

15
 check OCS ( I got some errors and warnings )

.

.

.

FATAL:
Atom .R<OAS 1>.A<H16 24> does not have a type

FATAL:
Atom .R<OAS 1>.A<H17 25> does not have a type

FATAL:
Atom .R<OAS 1>.A<H18 26> does not have a type

Warning:
Colse contact of 1.191413 angstroms between .R<OAS 1>.A<C1
1> and .R<OAS 1>.A<H1 2>

Warning:
Colse contact of 1.192445 angstroms between .R<OAS 1>.A<C1
1> and .R<OAS 1>.A<H2 3 >

Warning:
Colse contact of 1.192275 angstroms between .R<OAS 1>.A<C1
1> and .R<OAS 1>.A<H3 4>

.

.

.

Warning:
Colse contact of 1.192993 angstroms between .R<OAS 1>.A<C8
23> and .R<OAS 1>.A<H18 263>

parameters
for unit 'OCS'

for
bond parameters

for
angle parameters

Errors:
26 Warnings: 18

12
saveamberparams OCS h.prmtop h.inpcrd ( leap created EMPTY input
files )

13 Quit

--- On Thu, 12/4/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:
From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: AMBER: using packmol file in Amber
To: amber_at_scripps.edu
Date: Thursday, December 4, 2008, 10:32 AM

On Thu, Dec 04, 2008, oguz gurbulak wrote:

> I created a lib file and loaded it into leap . And also I generated a
> packmol pdb file and added TER cards into the packmol pdb file. But after
> I load packmol pdb file to leap , same errors and warnings happened. I
> attached the packmol pdb file. Could you please help me about this
problem?

This is really quite frustating to people reading this list, who would like
to help you. Here is what is missing:

1. You describe in pretty vague terms what you did ("created a lib
file",
"loaded it into leap", etc). But you don't say *exactly* what
you did, and
that is crucial.

2. You say you got the "same errors and warnings", but as far as I
can tell,
you never really posted those. In any event, you should re-post: most people
don't have the time to search back through the archives to find some old
error
messages. Plus, your previous posts referred to a residue named
"HEP", but the
current pdb file just has residues named "OAS". So, it's hard to
believe you
acutally got the "same" error messages.

3. Here's was my suggestion from before:

>
> Suggestion: start small, and work one step at a time. Be sure that you
can
> read and process a single HEP structure.

There's no indication that you tried that. If you can't load a single
molecule, you probably can't load multiple molecules.

Without knowing how you created the lib (and frcmod?) files, and without
knowing what the error messages are, no one will be able to help.

Sorry to come down hard on you, but problem reports need to be specific and
precise.

...dac
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