AMBER Archive (2006)

Subject: RE: AMBER: LEAP error (Test Case)

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Mon Oct 09 2006 - 10:37:18 CDT

Dear Dr. Case

I have been trying to run a GPCR simulation in a DMPC bilayer. For this, I
have downloaded a pre-equilibrated and hydrated bilayer from Dr. Phil
Biggin's tutorial from internet.

This file has 288 DMPC lipids and waters, and is in the PDB format. I intend
to convert it into amber top/crd file format to run simulation in amber9.
---------------------------------------------------------------------------
Antechamber
Since DMPC is a non-standard residue, I ran antechamber to get a prepi file
for the DMPC and named the residue DMP in the antechamber. I used a mol2
file as the input structure. The overall charge was neutral. The output file
was DMPC_bcc.prep

$ antechamber -rn DMP -i DMPC_mono_sybyl.mol2 -fi mol2 -o DMPC_bcc.prep -fo
prepi -c bcc

Then I used parmchk to check the parameters
$ parmchk -I DMP_bcc.prep -f prepi -o DMPC_frcmod
----------------------------------------------------------------------------

Leap

----------------------------------------------------------------------------
I had a complete DMPC bilayer file which was very big. So I thought first
trying to convert a smaller file to top/crd formats, if that works fine, I
can then convert my bigger file. So I retained just the first two DMPC
monomers of my original pdb file and 4 waters, in order to see how it
performs. That's how I created try2.pdb: it contains just 2 DMPC molecules
and 4 waters.

Now the Leap commands and error (in the end) are as follows >>>>>>>>>

r0914_at_redwood:/ptmp/r0914/Angi_trial/amber/dmpc_amber_preparation> tleap -s
-f leaprc.ff03
-I: Adding /usr/local/appl/amber9/dat/leap/prep to search path.
-I: Adding /usr/local/appl/amber9/dat/leap/lib to search path.
-I: Adding /usr/local/appl/amber9/dat/leap/parm to search path.
-I: Adding /usr/local/appl/amber9/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff03.

Welcome to LEaP!
Sourcing: /usr/local/appl/amber9/dat/leap/cmd/leaprc.ff03
Log file: ./leap.log
Loading parameters: /usr/local/appl/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /usr/local/appl/amber9/dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
Loading library: /usr/local/appl/amber9/dat/leap/lib/ions94.lib
Loading library: /usr/local/appl/amber9/dat/leap/lib/solvents.lib
Loading library: /usr/local/appl/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/appl/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/appl/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/appl/amber9/dat/leap/lib/all_amino03.lib
> source leaprc.gaff
----- Source: /usr/local/appl/amber9/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/appl/amber9/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/appl/amber9/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> loadamberprep DMPC_bcc.prep
Loading Prep file: ./DMPC_bcc.prep
> check DMP
Checking 'DMP'....
Checking parameters for unit 'DMP'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> try = loadpdb try2.pdb
Loading PDB file: ./try2.pdb
ERROR: Comparing atoms
        .R<DMP 1>.A<C1N 115>,
        .R<DMP 1>.A<H41 2>,
        .R<DMP 1>.A<H42 3>, and
        .R<DMP 1>.A<H43 4>
       to atoms
        .R<DMP 1>.A<C2M 5>,
        .R<DMP 1>.A<C1N 115>,
        .R<DMP 1>.A<H43 4>, and
        .R<DMP 1>.A<H41 2>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C2M from DMP did not match !
!
!ABORTING.
----------------------------------------------------------------------------

Like I previously mentioned, the input pdb file with just 1 DMPC molecule
and 4 waters perform fine in leap which is input_try1.pdb and its
corresponding output files are: try1.pdb, try1.prmtop, try1.inpcrd

PS: Since It is very difficult to manually edit the original 288 DMPC
molecules for placing TER cards between each residues and changing the atom
names (>50,000 atoms), I did not do that in this test case too. However, the
atom names for each DMPC and water residues are unique as is required by
leap.

I can send the original big DMPC file if required later.

I will look forward to your suggestions.

Thanks and Regards
Akshay Patny (Olemiss)
 

|-----Original Message-----
|From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
|David A. Case
|Sent: Sunday, October 08, 2006 11:29 PM
|To: amber_at_scripps.edu
|Subject: Re: AMBER: LEAP error
|
|On Fri, Oct 06, 2006, Akshay Patny wrote:
|
|> > try = loadpdb try2.pdb
|> Loading PDB file: ./try2.pdb
|> ERROR: Comparing atoms
|> .R<DMP 1>.A<C1N 115>,
|> .R<DMP 1>.A<H41 2>,
|> .R<DMP 1>.A<H42 3>, and
|> .R<DMP 1>.A<H43 4>
|> to atoms
|> .R<DMP 1>.A<C2M 5>,
|> .R<DMP 1>.A<C1N 115>,
|> .R<DMP 1>.A<H43 4>, and
|> .R<DMP 1>.A<H41 2>
|> This error may be due to faulty Connection atoms.
|> !FATAL ERROR----------------------------------------
|> !FATAL: In file [chirality.c], line 140
|> !FATAL: Message: Atom named C2M from DMP did not match !
|> !
|> !ABORTING.
|
|I think we will need to see the entire list of LEaP commands you used (try
|to make a test case that is as simple as possible.) In particular, we need
|to see whatever file you have that defines the DMP residue (prepin, mol2,
|etc.). The say in which "connection" atoms are defined is probably key
|to this problem. Also, please indicate how you constructed this DMP file.
|
|....thanks...dac
|...thanks...dac
|
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