[gmx-users] Re: pdb2gmx error
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 27 18:28:29 CEST 2012
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.
> ----- Original Message -----
> From: shounakb <baners4 at rpi.edu>
> To: gmx-users at gromacs.org
> Sent: Wednesday, June 27, 2012 8:39 PM
> Subject: [gmx-users] Re: pdb2gmx error
> C and O should go last (i.e. their atom numbers should be 14 and 15
> Hope this works!
> 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?
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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