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 <jalem...@vt.edu
<mailto:jalem...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto: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 <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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