[gmx-users] fatal error
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 22 22:07:44 CET 2011
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
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