[gmx-users] pdb2gmx

Sat Aug 20 07:58:24 CEST 2016

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.

>>
>> Message: 7
>> Date: Fri, 19 Aug 2016 15:30:14 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] pdb2gmx
>> Message-ID: <d8bcd9d8-b628-8e61-70e6-42e2dcca99da at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 8/19/16 10:52 AM, amitbehra at 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
>>
>> --
>> ==================================================
>>
>> 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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>
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