[gmx-users] Re: pdb2gmx error
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 27 18:44:54 CEST 2012
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.
> ----- Original Message -----
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> 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.
>> ----- 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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>> View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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