With Thanx,
Vivek
2008/8/13 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Every atom must be named appropriately, not just the first. Keep
making the appropriate changes.
-Justin
vivek sharma wrote:
Hi Justin,
Thanx again, your option worked for me now it is giving error
for the atom just next to PA (changed to AP) i.e. AO1 as
Processing chain 5 'E' (372 atoms, 9 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421
Fatal error:
Atom AO1 in residue NDPH 1 not found in rtp entry with 56 atoms
while sorting atoms
-------------------------------------------------------
following is the ligand atoms from the .rtp file
[ NADH ]
[ atoms ]
AP P 0.76000 0
AO1P OM -0.63500 0
AO2P OM -0.63500 0
AO5* OA -0.36000 0
O3P OA -0.26000 1
NP P 0.76000 1
NO1P OM -0.63500 1
NO2P OM -0.63500 1
NO5* OA -0.36000 1
AC5* CH2 0.00000 2
AC4* CH1 0.16000 3
AO4* OA -0.36000 3
AC1* CH1 0.20000 3
AN9 NR -0.20000 4
AC4 C 0.20000 4
AN3 NR -0.36000 5
AC2 CR1 0.36000 5
AN1 NR -0.36000 6
AC6 C 0.36000 6
AN6 NT -0.83000 7
AH61 H 0.41500 7
AH62 H 0.41500 7
AC5 C 0.00000 8
AN7 NR -0.36000 8
AC8 CR1 0.36000 8
AC2* CH1 0.15000 9
AO2* OA -0.54800 9
AH2* H 0.39800 9
AC3* CH1 0.15000 10
AO3* OA -0.54800 10
AH3* H 0.39800 10
NC5* CH2 0.00000 11
NC4* CH1 0.16000 12
NO4* OA -0.36000 12
NC1* CH1 0.20000 12
NN1 NR -0.20000 13
NC6 CR1 0.20000 13
NC2 CR1 0.00000 13
NC3 C 0.00000 13
NC4 CH2 0.00000 13
NC5 CR1 0.00000 13
NC7 C 0.38000 14
NO7 O -0.38000 14
NN7 NT -0.83000 15
NH71 H 0.41500 15
NH72 H 0.41500 15
NC2* CH1 0.15000 16
NO2* OA -0.54800 16
NH2* H 0.39800 16
NC3* CH1 0.15000 17
NO3* OA -0.54800 17
NH3* H 0.39800 17
And the corresponding atom listing from 1XU9.pdb is as...
HETATM 8111 AP NDPH 1 8.809 -4.754 22.676 1.00 12.71
HETATM 8112 AO1 NDPH 1 10.106 -4.137 23.158 1.00 11.98
HETATM 8113 AO2 NDPH 1 8.869 -5.751 21.580 1.00 13.09
HETATM 8114 O5B NDPH 1 8.010 -5.348 23.937 1.00 12.91
HETATM 8115 C5B NDPH 1 6.913 -6.239 23.752 1.00 12.91
HETATM 8116 C4B NDPH 1 6.493 -6.754 25.120 1.00 10.44
HETATM 8117 O4B NDPH 1 5.292 -7.535 24.969 1.00 13.02
HETATM 8118 C3B NDPH 1 7.588 -7.667 25.612 1.00 10.90
HETATM 8119 O3B NDPH 1 7.552 -7.543 27.047 1.00 12.99
HETATM 8120 C2B NDPH 1 7.086 -9.053 25.407 1.00 12.38
HETATM 8121 O2B NDPH 1 7.660 -10.046 26.246 1.00 13.11
HETATM 8122 C1B NDPH 1 5.579 -8.877 25.356 1.00 12.53
HETATM 8123 N9A NDPH 1 4.817 -9.905 24.673 1.00 11.65
HETATM 8124 C8A NDPH 1 5.033 -10.388 23.429 1.00 10.38
HETATM 8125 N7A NDPH 1 4.132 -11.360 23.119 1.00 11.50
HETATM 8126 C5A NDPH 1 3.332 -11.498 24.179 1.00 10.26
HETATM 8127 C6A NDPH 1 2.217 -12.337 24.568 1.00 11.19
HETATM 8128 N6A NDPH 1 1.746 -13.251 23.689 1.00 12.10
HETATM 8129 N1A NDPH 1 1.678 -12.169 25.805 1.00 11.24
HETATM 8130 C2A NDPH 1 2.130 -11.262 26.690 1.00 10.83
HETATM 8131 N3A NDPH 1 3.161 -10.439 26.428 1.00 10.06
HETATM 8132 C4A NDPH 1 3.776 -10.558 25.154 1.00 11.15
HETATM 8133 O3 NDPH 1 7.769 -3.631 22.173 1.00 12.62
HETATM 8134 PN NDPH 1 7.989 -2.036 22.130 1.00 12.08
HETATM 8135 O1N NDPH 1 8.430 -1.526 23.461 1.00 11.89
HETATM 8136 O2N NDPH 1 8.741 -1.692 20.889 1.00 11.73
HETATM 8137 O5D NDPH 1 6.467 -1.533 21.886 1.00 12.66
HETATM 8138 C5D NDPH 1 5.611 -1.361 23.020 1.00 11.65
HETATM 8139 C4D NDPH 1 4.298 -0.748 22.582 1.00 11.67
HETATM 8140 O4D NDPH 1 4.556 0.487 21.875 1.00 12.21
HETATM 8141 C3D NDPH 1 3.548 -1.649 21.637 1.00 11.97
HETATM 8142 O3D NDPH 1 2.175 -1.497 22.010 1.00 11.22
HETATM 8143 C2D NDPH 1 3.579 -0.984 20.290 1.00 12.02
HETATM 8144 O2D NDPH 1 2.475 -1.229 19.433 1.00 11.31
HETATM 8145 C1D NDPH 1 3.974 0.454 20.593 1.00 12.46
HETATM 8146 N1N NDPH 1 4.714 1.092 19.529 1.00 11.43
HETATM 8147 C2N NDPH 1 6.045 0.998 19.502 1.00 11.26
HETATM 8148 C3N NDPH 1 6.724 1.599 18.453 1.00 10.05
HETATM 8149 C7N NDPH 1 8.217 1.540 18.362 1.00 11.67
HETATM 8150 O7N NDPH 1 8.756 2.105 17.403 1.00 11.17
HETATM 8151 N7N NDPH 1 8.916 0.848 19.266 1.00 11.33
HETATM 8152 C4N NDPH 1 6.022 2.270 17.471 1.00 10.99
HETATM 8153 C5N NDPH 1 4.641 2.345 17.528 1.00 11.46
HETATM 8154 C6N NDPH 1 4.005 1.748 18.602 1.00 12.11
HETATM 8155 P2B NDPH 1 7.584 -11.626 25.952 1.00 13.18
HETATM 8156 O1X NDPH 1 8.540 -12.200 26.975 1.00 15.49
HETATM 8157 O2X NDPH 1 6.162 -12.049 26.180 1.00 13.31
HETATM 8158 O3X NDPH 1 8.073 -11.835 24.534 1.00 13.10
HETATM 8159 PA NDPH 2 -29.029 -5.471 7.894 1.00 12.85
HETATM 8160 O1A NDPH 2 -30.208 -4.995 7.102 1.00 13.51
HETATM 8161 O2A NDPH 2 -29.200 -5.823 9.322 1.00 11.99
HETATM 8162 O5B NDPH 2 -28.355 -6.688 7.107 1.00 11.99
HETATM 8163 C5B NDPH 2 -27.299 -7.469 7.665 1.00 12.75
HETATM 8164 C4B NDPH 2 -27.105 -8.686 6.774 1.00 11.47
now trick is not working for atom next to PA, please tell me if
there is any thing should be taken care while doing so.
sorry for cribbing you again and again, but I am helpless in
this field.
Please suggest
With Thanx,
Vivek
2008/8/13 Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>
vivek sharma wrote:
Hi Justin,
Thanx for your suggestion. But, I am not getting how to do
correction in those files I am using gromacs 3.3.3 and
1XU9.pdb
molecule for my simulation.
I am not getting what is happening in the
simulation...:(...:(
kindly suggest.
I'm guessing that NDP is the NADPH cofactor, which in Gromos96
language is called NDPH (that's what pdb2gmx is trying to
call, it
as well). What's happening is you've got the atoms present for
NADPH, but the force field simply has different names for the
atoms.
The simple fix is to re-name the atoms in the .pdb file
according to
how they appear in the .rtp entry for NADPH (called NDPH). For
example, the two phosphorus atoms in the phosphodiester
between the
adenosine and nicotinamide moieties are called AP and NP. AP
corresponds to the P atom in the phosphate donated by the
adenoside
system; NP corresponds to the P atom from the nicotinamide
phosphate. You've got an atom called PA instead, which is
probably
equivalent to AP (but do check, because that's just a guess
from my
end).
-Justin
With Thanx,
Vivek
2008/8/13 Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>>>
There are two potential solutions to this error. For
background,
refer to:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
So your options are:
1. If the ligand is present in the .rtp file, make
sure your atom
nomenclature corresponds to that of the force field.
2. Remove the ligand and deal with its topology separately
(search
Google for John Kerrigan's tutorial for enzyme-ligand
systems).
-Justin
vivek sharma wrote:
Hi Nahren,
Thanx for your help, I opened the pdb file with
swisspdb
viewer
and then tried the pdb2gmx command over that pdb
file and got
the following error.
Total mass 28295.072 a.m.u.
Total charge 1.000 e
Writing topology
Processing chain 5 'E' (372 atoms, 9 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: 'NDP' not found in residue topology database,
trying to
use 'NDPH'
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421
Fatal error:
Atom PA in residue NDPH 1 not found in rtp entry
with 56
atoms
while sorting atoms
-------------------------------------------------------
and the error for the all atom forcefield were as
follow.
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 436
Fatal error:
Residue 'NDP' not found in residue topology database
-------------------------------------------------------
any advice for this will be of great help
for me.
Thanx,
Vivek
2008/8/12 nahren manuel <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
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<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
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Dear Vivek,
you just have to download swisspdb and open
your pdb file.
Thats all
you got to do and It is more than enough. If
you have more
than 2/3
residues missing then, make sure the Ramachandran
plots are fine.
Also try a simple minimization before begining
gromacs.
nahren
--- On *Tue, 8/12/08, vivek sharma
/<[EMAIL PROTECTED]
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From: vivek sharma
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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Subject: Re: [gmx-users] Error in
pdb2gmx.....Atom CE2
not found
in residue PHE270 while adding hydrogens
To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
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<mailto:gmx-users@gromacs.org>>>>>
Date: Tuesday, August 12, 2008, 6:34 PM
Hi David,
Thanx a lot again. can you please tell me the
criteria or the
standards to do such correction or can you
suggest
some
link or
tutorial for the same?
whether swiss pdb can help in such cases?
With Thanx,
Vivek
2008/8/12 David van der Spoel
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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vivek sharma wrote:
Hi There,
I am new to molecular dynamics and
GROMACS.
While trying MD for 1XU9.pdb (pdbid) in
the very 1st
step on using the command....
pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p
1XU9.top -i
1XU9.itp
-vsite hydrogen -water spce
I got the following in the last of
error.....
......
......
......
.......
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in
residue 270
while
adding atom
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304
Fatal error:
Atom CE2 not found in residue
PHE270 while
adding
hydrogens
-------------------------------------------------------
I tried the same with different force
field and
water
models, but getting the same error
again
and again.
any suggestion will be highly
appreciated.
You have an incorrect pdb file. An atom is
missing.
You have
to fix it yourself.
With thanx,
Vivek
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
<http://vt.edu> | (540)
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
========================================
