[gmx-users] error after new addition of molecule
Rahul Karyappa
r.karyappa at ncl.res.in
Wed Aug 17 13:43:15 CEST 2005
Thank you for your lind reply. Your information worked and I am able to
run pdb2gmx command. But when I ran grompp command it geve me following
error:
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
WARNING 1 [file "topol1.top", line 54]:
No default Bond types, using zeroes
WARNING 2 [file "topol1.top", line 55]:
No default Bond types, using zeroes
WARNING 3 [file "topol1.top", line 56]:
No default Bond types, using zeroes
WARNING 4 [file "topol1.top", line 57]:
No default Bond types, using zeroes
WARNING 5 [file "topol1.top", line 58]:
No default Bond types, using zeroes
WARNING 6 [file "topol1.top", line 59]:
No default Bond types, using zeroes
WARNING 7 [file "topol1.top", line 60]:
No default Bond types, using zeroes
WARNING 8 [file "topol1.top", line 61]:
No default Bond types, using zeroes
WARNING 9 [file "topol1.top", line 62]:
No default Bond types, using zeroes
WARNING 10 [file "topol1.top", line 76]:
No default Angle types, using zeroes
Cleaning up temporary file gromppHDlOEd
Fatal error: Too many warnings, grompp terminated
Generated .top file looks like as follows:
; File 'topol1.top' was generated
; By user: root (0)
; On host: fox
; At date: Wed Aug 17 17:18:57 2005
;
; This is your topology file
; "Stop Drinking My Beer !" (The Amps)
;
; Include forcefield parameters
#include "ffgmx.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr
residue atom cgnr
charge mass
typeB chargeB massB
1
C 1
PE CAA
1 -0.2913 12.011
; qtot -0.2913
2
H 1
PE HAA1
1
0 1.008 ; qtot -0.2913
3
H 1
PE HAA2
1 0.145
1.008 ; qtot -0.1463
4
H 1
PE HAA3
1 0.145
1.008 ; qtot -0.0013
5
C 1
PE CAB
1 -0.2888 12.011
; qtot -0.2901
6
H 1
PE HAB1
1 0.1451
1.008 ; qtot -0.145
7
H 1
PE HAB2
1 0.1451
1.008 ; qtot 9.999e-05
8
C 1
PE CAC
1 -0.2913 12.011
; qtot -0.2912
9
H 1
PE HAC1
1 0.145
1.008 ; qtot -0.1462
10
H 1
PE HAC2
1 0.145
1.008 ; qtot -0.0012
11
C 1
PE CAD
1 -0.2888 12.011
; qtot -0.29
12
H 1
PE HAD1
1 0.1451
1.008 ; qtot -0.1449
13
H 1
PE HAD2
1 0.1451
1.008 ; qtot 0.0002
14
C 1
PE CAE
1 -0.2913 12.011
; qtot -0.2911
15
H 1
PE HAE1
1 0.145
1.008 ; qtot -0.1461
16
H 1
PE HAE2
1 0.145
1.008 ; qtot -0.0011
17
C 1
PE CAF
1 -0.2888 12.011
; qtot -0.2899
18
H 1
PE HAF1
1 0.1451
1.008 ; qtot -0.1448
19
H 1
PE HAF2
1 0.1451
1.008 ; qtot 0.0003
20
C 1
PE CAG
1 -0.2913 12.011
; qtot -0.291
21
H 1
PE HAG1
1 0.145
1.008 ; qtot -0.146
22
H 1
PE HAG2
1 0.145
1.008 ; qtot -0.001
23
C 1
PE CAH
1 -0.2888 12.011
; qtot -0.2898
24
H 1
PE HAH1
1 0.1451
1.008 ; qtot -0.1447
25
H 1
PE HAH2
1 0.1451
1.008 ; qtot 0.0003999
26
C 1
PE CAI
1 -0.2913 12.011
; qtot -0.2909
27
H 1
PE HAI1
1 0.145
1.008 ; qtot -0.1459
28
H 1
PE HAI2
1 0.145
1.008 ; qtot -0.0009001
29
C 1
PE CAJ
1 -0.2888 12.011
; qtot -0.2897
30
H 1
PE HAJ1
1
0 1.008 ; qtot -0.2897
31
H 1
PE HAJ2
1 0.1451
1.008 ; qtot -0.1446
32
H 1
PE HAJ3
1 0.1451
1.008 ; qtot 0.0004999
[ bonds ]
; ai aj
funct
c0
c1
c2 c3
1 5 1
5 8 1
8 11 1
11 14 1
14 17 1
17 20 1
20 23 1
23 26 1
26 29 1
[ pairs ]
; ai aj
funct
c0
c1
c2 c3
1 11 1
5 14 1
8 17 1
11 20 1
14 23 1
17 26 1
20 29 1
[ angles ]
; ai aj ak
funct
c0
c1
c2 c3
1 5 8 1
5 8 11 1
8 11 14 1
11 14 17 1
14 17 20 1
17 20 23 1
20 23 26 1
23 26 29 1
[ dihedrals ]
; ai aj ak
al
funct
c0
c1
c2
c3
c4 c5
1 5 8 11 1
5 8 11 14 1
8 11 14 17 1
11 14 17 20 1
14 17 20 23 1
17 20 23 26 1
20 23 26 29 1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct
fcx
fcy fcz
1 1
1000
1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein 1
Please suggest for this. Thanking you once again.
Rahul karyappa
NCL, Pune
India
-- Original Message --
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Wed, 17 Aug 2005 11:53:18 +0200
Subject: Re: [gmx-users] error after new addition of molecule
On Wed, 2005-08-17 at 14:56 +0530, Rahul Karyappa wrote:
> Dear all,
> I wanted to add a new molecule in the forcefield database. For a
> trial I took a 10 repeat unit chain of Polyethylene. So I added it to
> the residue database and also in the aminoacids.dat file. When I ran
> pdb2gmx command to generate .gro and .top file but it gave me
> following error:
>
> Fatal error: atom N not found in residue 1PE while combining tdb and
> rtp
>
> How should I proceed next? Can anyone have suggestions for this error?
pdb2gmx -ter
select none for termini
> Thanking you all.
>
> Rahul Karyappa
> NCL, Pune
> India
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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