AMBER Archive (2004)

Subject: AMBER: Re: ANAL problem

From: A.B.S.M Osman gani (osman_gani1974_at_yahoo.com)
Date: Wed Feb 04 2004 - 13:31:18 CST

David,
Thank you for your mail.
1)I have used same prmtop file for running dynamics.
2) These (4052, 4047, 4048, and 4050) are the Ligand atoms in my Protein+Ligand complex such as H7,C1,C2 and N4 respectively of Pyrazole.When I saw the Pyrazole molecule (in complex with protein) with DEEP VIEW, I saw omega,phi,psi all to be 1000.00 at all atoms in pyrazole.
3) With ptraj, the script was:
trajin ../mdcrd6
trajout pyrdock restart nobox nowrap
go

where mdcrd6 is the mdcrd of last dynamics run.
4) Following are the first few lines of my prmtop file.
%VERSION VERSION_STAMP = V0001.000 DATE = 11/04/03 20:03:13
%FLAG TITLE
%FORMAT(20a4)
 
%FLAG POINTERS
%FORMAT(10I8)
   27373 22 25356 2058 4632 2812 8636 5285 0 0
   53557 8030 2058 2812 5285 79 161 67 51 1
       0 0 0 0 0 0 0 2 70 0
       0
%FLAG ATOM_NAME
%FORMAT(20a4)
N H1 H2 H3 CA HA CB HB2 HB3 CG HG2 HG3 SD CE HE1 HE2 HE3 C O N
H CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB2 HB3 CG HG
CD1 HD11HD12HD13CD2 HD21HD22HD23C O N H CA HA CB HB CG2 HG21HG22HG23
OG1 HG1 C O N H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O N H
CA HA CB HB2 HB3 CG HG2 HG3 CD HD2 HD3 CE HE2 HE3 NZ HZ1 HZ2 HZ3 C O
N H CA HA CB HB2 HB3 CG OD1 ND2 HD21HD22C O N H CA HA CB HB
CG1 HG11HG12HG13CG2 HG21HG22HG23C O N H CA HA CB HB CG2 HG21HG22HG23
"xwation.top" 62853L, 5089617C 1,1 Top

6) For other ligands (more atoms than pyrazole) everything was ok (I mean upto ANAL calculation of energy).

7) I guess, I have made some blunder in parameterization while docking(ICM was used for docking) but I am not sure.

Regards,

Osman

On Thu, Jan 29, 2004, A.B.S.M Osman gani wrote:
>
> I have been using AMBER 7 on Red Hat Linux. I have done long dynamic
> simulations in SANDER for a ligand +Protein complex. Then trajectories were
> extracted with ?ptraj?. For energy analysis, ANAL command was performed.
> But the anal output file shows ?DIHEDRAL ANGLE ERROR: 1 12153
> 12138 12141 12147 5 0 0.0000 0.0000?
>

You have a bad dihedral, but it is not clear whether this is really in the
prmtop file, or whether the anal program is overflowing some array.

The program thinks that the first dihedral, which involves atoms
4052, 4047, 4048, and 4050, (dihedral code "5") has a periodicity of 0;
this is illegal.

Are you using the exact same prmtop file that you used for the dynamics run?
Is there anything special about the above atoms? You say that the
"trajectories were extracted with ptraj", but it is not clear what exactly
you did with ptraj.

You might examine your prmtop file (either by hand, or with rdparm) to look
at the dihedral angles. Also, please post the first ten lines or so of
your prmtop file: it is certainly possible that you are exceeding some
maximum value in anal (you have a very big system) that is not being trapped.

..regards...dac 

-- 

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