[gmx-users] pdb2gmx
Justin Lemkul
jalemkul at vt.edu
Sat Aug 20 13:16:37 CEST 2016
On 8/20/16 1:57 AM, amitbehra at 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 <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
>>>
>>> ==================================================
>>
>>
>>
>> ------------------------------
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a mail to gmx-users-request at gromacs.org.
>>
>> End of gromacs.org_gmx-users Digest, Vol 148, Issue 79
>> ******************************************************
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>
--
==================================================
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
==================================================
More information about the gromacs.org_gmx-users
mailing list