[gmx-users] Atom N not found....
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Apr 6 13:08:33 CEST 2012
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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