I think I need to edit the aminoacids.rtp file in gromos43a1.ff folder as
far as I understand from mailing list. I am using 43a1 forcefield. I do not
understand what kind of changes should I do.
*the aminoacids.rtp file:*
[ ACE ]
[ atoms ]
CA CH3 0.000 0
C C 0.380 1
O O -0.380 1
[ bonds ]
C CA gb_26
C O gb_4
C +N gb_9
[ angles ]
CA C O ga_30
CA C +N ga_18
O C +N ga_32
[ 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_8
[ angles ]
-O -C N ga_32
-CA -C N ga_18
-C N H1 ga_22
-C N H2 ga_22
H1 N H2 ga_23
[ dihedrals ]
-CA -C N H1 gd_4
[ impropers ]
-C -O N -CA gi_1
N H1 H2 -C gi_1
[ ALA ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH3 0.00000 1
C C 0.380 2
O O -0.380 2
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
2011/1/21 Justin A. Lemkul <jalem...@vt.edu>
>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> Gromacs 4.5.3
>> pdb2gmx -f xxx.pdb -water spc
>> select Force Field:9
>> *Fatal error:*
>> atom C not found in buiding block 13NH2 while combining tdb and rtp
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> How can I fixed this error?
>>
>>
> You have a carbon atom in a residue that should only contain NH2. Refer to
> the .rtp file for what is expected, then make a suitable structure that
> conforms to those requirements.
>
> This has been asked and answered hundreds of times, so please make use of
> the mailing list search. You would have gotten your answer in minutes
> rather than hours.
>
> -Justin
>
>
> Thanks in advance
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ========================================
>
> 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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--
Ahmet YILDIRIM
--
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