rama david wrote:
HI all ,
sorry for above incomplete information ,
I change CH3 of ACE residue of my pdb file to CA .
The formatting of a .pdb file requires fixed spacing. By turning CH3 into CA
(which is correct), you deleted a space such that instead of finding 'ACE' as
the residue name, pdb2gmx is finding 'CE' since it has been shifted to the left
one space. Fix the spacing and you fix your problem.
-Justin
Thank you in advance
On Fri, Apr 6, 2012 at 5:34 PM, rama david <ramadavidgr...@gmail.com
<mailto:ramadavidgr...@gmail.com>> wrote:
Hi GROMACS Friends and Mark..
Thank you for reply ...
My command line is
pdb2gmx -f ....pdb -o p.pdb -p p.top -ignh -ter
I choose the G96 53a6 ff , along with spc water model.
Select start terminus type for ACE-1
0: NH3+
1: NH2
2: None
2
Start terminus ACE-1: None
Select end terminus
0: COO-
1: COOH
2: None
0
End terminus : COO-
So I got the following out put...
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c,
line: 655
Fatal error:
Atom CH3 in residue ACE 1 was not found in rtp entry ACE with 3 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I have the limited experience for these problem..
Can you tell me what to do in such conditions????
I change the Atom CH3 in pdb to CA and proceed with the above
command line
and option .
I got the following error
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c,
line: 581
Fatal error:
Residue 'CE' not found in residue topology database
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I have the limited experience for these problem..
Can you tell me what to do in such conditions????
On Fri, Apr 6, 2012 at 4:38 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 6/04/2012 9:05 PM, Mark Abraham wrote:
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.
... and if you'd also shown the last piece of your pdb2gmx
output and given us the whole command line you used, then you'd
have gotten your answer faster and wasted less of people's time
guessing what the real problem was.
Mark
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--
========================================
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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