On 6/27/12 12:43 PM, Shima Arasteh wrote:
I know that no missing atom is here.
As the fatal error is about atom name CA, I checked it, but it's actually
existed in both .rtp and pdb in agreement.
Please help me, I don't know what to do :(
Please copy and paste the entirety of the first three residues in your .pdb file
so we can see what you're working with.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin A. Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Cc:
Sent: Wednesday, June 27, 2012 8:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 12:25 PM, Shima Arasteh wrote:
You mean the order of C and O should be changed in .pdb file? If yes, it didn't
work!
The order of atoms in the .pdb file is irrelevant. What may be the issue is
that when pdb2gmx is reporting the error, it is printing its own internal
residue number (i.e., the second residue in the chain) - are you missing residue
1? Files downloaded from the PDB are also convenient because they report all
missing atoms with "MISSING" entries in the header of the file. These entries
will indicate problems before even running pdb2gmx.
-Justin
Sincerely,
Shima
----- Original Message -----
From: shounakb <bane...@rpi.edu>
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, June 27, 2012 8:39 PM
Subject: [gmx-users] Re: pdb2gmx error
Hi,
C and O should go last (i.e. their atom numbers should be 14 and 15
respectively.
Hope this works!
Regards,
Shounak
Shima Arasteh wrote
Hi all,
I got this error :
Atom CA is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue number 2.
I checked the pdb file and rtp file.
.rtp file:
[ SER ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA CH1 0.000 1
CB CH2 0.150 2
OG OA -0.548 2
HG HO 0.398 2
C C 0.380 3
O O -0.380 3
.pdb file:
ATOM 10 N SER 2 -3.181 3.235 3.442
ATOM 11 CA SER 2 -3.363 4.671 3.524
ATOM 12 C SER 2 -4.135 5.054 4.778
ATOM 13 O SER 2 -5.272 4.628 4.966
ATOM 14 CB SER 2 -4.138 5.196 2.320
ATOM 15 OG SER 2 -4.296 6.612 2.437
I guess they are in agreement, so what's the problem?
Sincerely,
Shima
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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