On 6/04/2012 8:27 PM, rama david wrote:
Hi Gromacs Friends and Justin ,
Thank you for reply and suggestion.
These is short part of my PDB .
ATOM 1 1H ACE 1 0.000 0.000 0.000
ATOM 2 CH3 ACE 1 0.000 1.090 0.000
ATOM 3 2H ACE 1 1.028 1.453 -0.000
ATOM 4 3H ACE 1 -0.514 1.453 -0.890
ATOM 5 C ACE 1 -0.721 1.600 1.249
ATOM 6 O ACE 1 -0.839 2.806 1.453
ATOM 7 N PRO 2 -1.227 0.727 2.126
ATOM 8 CA PRO 2 -1.918 1.181 3.321
ATOM 9 HA PRO 2 -2.553 2.031 3.073
ATOM 10 C PRO 2 -0.928 1.587 4.404
ATOM 11 O PRO 2 -1.069 2.645 5.013
ATOM 12 CB PRO 2 -2.782 0.075 3.851
ATOM 13 1HB PRO 2 -2.469 -0.177 4.864
ATOM 14 2HB PRO 2 -3.822 0.401 3.862
ATOM 15 CG PRO 2 -2.645 -1.140 2.964
ATOM 16 1HG PRO 2 -2.232 -1.966 3.542
ATOM 17 2HG PRO 2 -3.606 -1.451 2.556
ATOM 18 CD PRO 2 -1.680 -0.755 1.882
ATOM 19 1HD PRO 2 -2.173 -0.830 0.913
ATOM 20 2HD PRO 2 -0.816 -1.419 1.895
ATOM 21 N GLY 3 0.076 0.740 4.644
ATOM 22 H GLY 3 0.135 -0.114 4.109
ATOM 23 CA GLY 3 1.083 1.012 5.650
The gromacs96 53a6 .rtp file mention the following data...
bondedtypes ]
; bonds angles dihedrals impropers
2 2 1 2
[ ACE ]
[ atoms ]
CA CH3 0.000 0
C C 0.450 1
O O -0.450 1
[ bonds ]
C CA gb_27
C O gb_5
C +N gb_19
[ angles ]
CA C O ga_30
CA C +N ga_19
O C +N ga_33
[ 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_9
[ angles ]
-O -C N ga_33
-CA -C N ga_19
-C N H1 ga_23
-C N H2 ga_23
H1 N H2 ga_24
[ dihedrals ]
-CA -C N H1 gd_14
[ impropers ]
-C -O N -CA gi_1
N H1 H2 -C gi_1
As per my pdb file N atom is the part of PROLINE , not the ACE...
I got the topology by using the Amber 03 FF.
But my priority is to the GROMOS96 53a6 force field ...
Could any suggest me the way to tackle these problem???
The default is to try to put termini on the protein chain. Your chain
already has them, so you need to tell pdb2gmx not to try to add termini.
See pdb2gmx -h.
Mark
With Best Wishes,
R.Davaid
On Thu, Apr 5, 2012 at 4:13 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
rama david wrote:
Hi Gromacs friends,
When I given the command ...
pdb2gmx -f .. -o .. -p .. -ignh
I gate the following error..
------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file:
/build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1070
Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
When I goes through the detail of the website at
http://www.gromacs.org/Documentation/Errors and document
I come to know that I have to modify the rtp file,
Nowhere in the explanation of the error does it suggest that you
should alter the .rtp file in this instance. You have atoms in
your structure that are not in the .rtp entry. Specifically, your
structure file has an N atom in ACE, but ACE only contains CA, C,
and O. The N atom should be the first atom in the next residue,
not ACE.
-Justin
--
========================================
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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