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