[gmx-users] Atom N not found....
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 6 15:06:15 CEST 2012
rama david wrote:
> HI all ,
> sorry for above incomplete information ,
> I change CH3 of ACE residue of my pdb file to CA .
>
The formatting of a .pdb file requires fixed spacing. By turning CH3 into CA
(which is correct), you deleted a space such that instead of finding 'ACE' as
the residue name, pdb2gmx is finding 'CE' since it has been shifted to the left
one space. Fix the spacing and you fix your problem.
-Justin
> Thank you in advance
>
> On Fri, Apr 6, 2012 at 5:34 PM, rama david <ramadavidgroup at gmail.com
> <mailto:ramadavidgroup at gmail.com>> wrote:
>
> Hi GROMACS Friends and Mark..
>
> Thank you for reply ...
> My command line is
> pdb2gmx -f ....pdb -o p.pdb -p p.top -ignh -ter
> I choose the G96 53a6 ff , along with spc water model.
>
> Select start terminus type for ACE-1
> 0: NH3+
> 1: NH2
> 2: None
> 2
> Start terminus ACE-1: None
>
> Select end terminus
> 0: COO-
> 1: COOH
> 2: None
> 0
> End terminus : COO-
>
> So I got the following out put...
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c,
> line: 655
>
> Fatal error:
> Atom CH3 in residue ACE 1 was not found in rtp entry ACE with 3 atoms
> while sorting atoms.
>
> .
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I have the limited experience for these problem..
> Can you tell me what to do in such conditions????
>
> I change the Atom CH3 in pdb to CA and proceed with the above
> command line
> and option .
> I got the following error
>
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c,
> line: 581
>
> Fatal error:
> Residue 'CE' not found in residue topology database
>
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I have the limited experience for these problem..
> Can you tell me what to do in such conditions????
>
>
> On Fri, Apr 6, 2012 at 4:38 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 6/04/2012 9:05 PM, Mark Abraham wrote:
>> On 6/04/2012 8:27 PM, rama david wrote:
>>> Hi Gromacs Friends and Justin ,
>>>
>>> Thank you for reply and suggestion.
>>>
>>> These is short part of my PDB .
>>>
>>> ATOM 1 1H ACE 1 0.000 0.000 0.000
>>> ATOM 2 CH3 ACE 1 0.000 1.090 0.000
>>> ATOM 3 2H ACE 1 1.028 1.453 -0.000
>>> ATOM 4 3H ACE 1 -0.514 1.453 -0.890
>>> ATOM 5 C ACE 1 -0.721 1.600 1.249
>>> ATOM 6 O ACE 1 -0.839 2.806 1.453
>>> ATOM 7 N PRO 2 -1.227 0.727 2.126
>>> ATOM 8 CA PRO 2 -1.918 1.181 3.321
>>> ATOM 9 HA PRO 2 -2.553 2.031 3.073
>>> ATOM 10 C PRO 2 -0.928 1.587 4.404
>>> ATOM 11 O PRO 2 -1.069 2.645 5.013
>>> ATOM 12 CB PRO 2 -2.782 0.075 3.851
>>> ATOM 13 1HB PRO 2 -2.469 -0.177 4.864
>>> ATOM 14 2HB PRO 2 -3.822 0.401 3.862
>>> ATOM 15 CG PRO 2 -2.645 -1.140 2.964
>>> ATOM 16 1HG PRO 2 -2.232 -1.966 3.542
>>> ATOM 17 2HG PRO 2 -3.606 -1.451 2.556
>>> ATOM 18 CD PRO 2 -1.680 -0.755 1.882
>>> ATOM 19 1HD PRO 2 -2.173 -0.830 0.913
>>> ATOM 20 2HD PRO 2 -0.816 -1.419 1.895
>>> ATOM 21 N GLY 3 0.076 0.740 4.644
>>> ATOM 22 H GLY 3 0.135 -0.114 4.109
>>> ATOM 23 CA GLY 3 1.083 1.012 5.650
>>>
>>> The gromacs96 53a6 .rtp file mention the following data...
>>>
>>> bondedtypes ]
>>> ; bonds angles dihedrals impropers
>>> 2 2 1 2
>>>
>>> [ ACE ]
>>> [ atoms ]
>>> CA CH3 0.000 0
>>> C C 0.450 1
>>> O O -0.450 1
>>> [ bonds ]
>>> C CA gb_27
>>> C O gb_5
>>> C +N gb_19
>>> [ angles ]
>>> CA C O ga_30
>>> CA C +N ga_19
>>> O C +N ga_33
>>> [ impropers ]
>>> C CA +N O gi_1
>>>
>>> [ NH2 ]
>>> [ atoms ]
>>> N NT -0.83 0
>>> H1 H 0.415 0
>>> H2 H 0.415 0
>>> [ bonds ]
>>> N H1 gb_2
>>> N H2 gb_2
>>> -C N gb_9
>>> [ angles ]
>>> -O -C N ga_33
>>> -CA -C N ga_19
>>> -C N H1 ga_23
>>> -C N H2 ga_23
>>> H1 N H2 ga_24
>>> [ dihedrals ]
>>> -CA -C N H1 gd_14
>>> [ impropers ]
>>> -C -O N -CA gi_1
>>> N H1 H2 -C gi_1
>>>
>>> As per my pdb file N atom is the part of PROLINE , not the ACE...
>>> I got the topology by using the Amber 03 FF.
>>> But my priority is to the GROMOS96 53a6 force field ...
>>>
>>> Could any suggest me the way to tackle these problem???
>>
>> The default is to try to put termini on the protein chain.
>> Your chain already has them, so you need to tell pdb2gmx not
>> to try to add termini. See pdb2gmx -h.
>
> ... and if you'd also shown the last piece of your pdb2gmx
> output and given us the whole command line you used, then you'd
> have gotten your answer faster and wasted less of people's time
> guessing what the real problem was.
>
> Mark
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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