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]>>
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]> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>
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] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>/* wrote:
From: vivek sharma <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>
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>>>
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]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>>
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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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