[gmx-users] Re: pdb2gmx error
shima_arasteh2001 at yahoo.com
Wed Jun 27 18:25:01 CEST 2012
You mean the order of C and O should be changed in .pdb file? If yes, it didn't work!
----- 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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