[gmx-users] fatal error
ahmet yıldırım
ahmedo047 at gmail.com
Sat Jan 22 22:17:43 CET 2011
Thank you very much
22 Ocak 2011 23:07 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:
>
>
> ahmet yıldırım wrote:
>
>> please look at the attached file
>>
>>
> I had no problem making a topology.
>
> $ pdb2gmx -f 3MOA.pdb -ter
>
> ...
> Using the Gromos43a1 force field in directory gromos43a1.ff
> ...
> Select start terminus type for GLU-659
> 0: NH3+
> 1: NH2
> 2: None
> 0
> Start terminus GLU-659: NH3+
> Select end terminus type for NH2-671
> 0: COO-
> 1: COOH
> 2: None
> 2
> End terminus NH2-671: None
> Checking for duplicate atoms....
> Now there are 13 residues with 139 atoms
> Chain time...
> ...
> Select start terminus type for LEU-2
> 0: NH3+
> 1: NH2
> 2: None
> 0
> Start terminus LEU-2: NH3+
> Select end terminus type for CYS-214
> 0: COO-
> 1: COOH
> 2: None
> 0
> End terminus CYS-214: COO-
> ...
> Select start terminus type for ARG-1
> 0: NH3+
> 1: NH2
> 2: None
> 0
> Start terminus ARG-1: NH3+
> Select end terminus type for ASP-217
> 0: COO-
> 1: COOH
> 2: None
> 0
> End terminus ASP-217: COO-
> ...
>
> -Justin
>
> 22 Ocak 2011 22:54 tarihinde Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> jalemkul at vt.edu>> yazdı:
>>
>>
>>
>>
>> ahmet yıldırım wrote:
>>
>> 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
>>
>>
>> Please post your .pdb file.
>>
>> -Justin
>>
>>
>> 22 Ocak 2011 00:45 tarihinde Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>> <mailto: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>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>
>> <mailto: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>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>> <mailto: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> <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> <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> <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
>>
>> ========================================
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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
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>
--
Ahmet YILDIRIM
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