On 8/20/16 1:57 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hi Justin,
Here is the full screen output:
Read 2236 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 285 residues with 2236 atoms
chain #res #atoms
1 ' ' 285 2236
All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 (2236 atoms, 285 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 412 donors and 445 acceptors were found.
There are 574 hydrogen bonds
Will use HISE for residue 292
Identified residue LYS8 as a starting terminus.
Identified residue HIS292 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET70 CYS87 MET270 MET281 CYS285
SD500 SG649 SD2051 SD2135 SG2165
CYS87 SG649 2.813
MET270 SD2051 5.200 2.414
MET281 SD2135 3.579 0.855 1.703
CYS285 SG2165 3.012 0.370 2.301 0.930
HIS292 NE22232 1.990 1.007 3.388 1.772 1.152
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c,
line: 127
Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
First it was N, now it's CA? What happened to the error about N? Only the
first missing atom should trigger a fatal error. There's nothing obvious to me
from the provided information about why it's failing, so check to make sure CA
isn't missing, make sure that the PDB file is correctly formatted, and also
consider your residue names. AMBER uses N- and C-prefixed residues for termini
(e.g. NLYS instead of LYS, CHIS instead of HIS) so you may have to manually
rename the residues unless pdb2gmx does some magic under the hood (it may, I
haven't checked in a while since I don't use the AMBER force fields).
-Justin
Message: 7
Date: Fri, 19 Aug 2016 15:30:14 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pdb2gmx
Message-ID: <d8bcd9d8-b628-8e61-70e6-42e2dcca9...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello users,
I am using pdb2gmx on a protein.
Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
ATOM 1 N LYS 8 59.565 44.696 51.226 1.00 0.00
N
0.00 H
ATOM 19 NZ LYS 8 62.201 50.111 51.767 1.00 0.00
N
These are N atoms in my LYS . Can anyone point out what the problem.
Please provide your exact pdb2gmx command and the full screen output.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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