[gmx-users] fatal error
ahmet yıldırım
ahmedo047 at gmail.com
Sat Jan 22 21:53:52 CET 2011
Dear Justin,
I manually specify termini. I choosed "None" but I have the same error.
Fatal error:
atom C not found in residue 13NH2 while combining tdb and rtp
22 Ocak 2011 00:45 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear justin,
>>
>> I looked at the pdb file. No NH2 reside contains carbon atom.
>>
>> What should I do?
>>
>
> In this case, you need to manually specify termini. Choose "None" to allow
> your capping groups to be built properly.
>
> -Justin
>
>
>> 22 Ocak 2011 00:18 tarihinde Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> yazdı:
>>
>>
>>
>>
>> ahmet yıldırım wrote:
>>
>> 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.
>>
>>
>> You do not need to modify the .rtp file, you need to modify your
>> coordinate file, as I said before. The fatal error indicates that
>> you have included a C atom in an NH2 residue, which is just a
>> neutral amine and contains no carbon, as should be clear from the
>> .rtp file.
>>
>> -Justin
>>
>> *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 <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>>
>> <mailto:jalemkul at 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 <http://vt.edu> <http://vt.edu> | (540)
>>
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
>>
>>
>> -- 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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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>> Please search the archive at
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>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
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>
--
Ahmet YILDIRIM
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