[gmx-users] Atom N not found....
rama david
ramadavidgroup at gmail.com
Sat Apr 7 06:35:24 CEST 2012
Hi Justin ,
Thank you , You are right .
Problem get solved by change in spacing in PDB file.
have a nice day.
With Best Wishes,
R.David
On Fri, Apr 6, 2012 at 6:36 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <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<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<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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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