[gmx-users] trjconv index mismatch
Alex
nedomacho at gmail.com
Tue Apr 19 01:39:36 CEST 2016
The atom groups, as they appear in the coordinate input, are:
1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions
I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):
step 1:
gmx convert-tpr -s prod.tpr -o cnt_only.tpr
selected CNT
step 2:
trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb
this last one does not even bother to open the menu, it throws the
following:
-------------------------------------------------------
Program trjconv, VERSION 5.0.5
Source code file:
/home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line:
957
Software inconsistency error:
Position restraint coordinates are missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Any thoughts?
On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/18/16 7:27 PM, Alex wrote:
>
>> Yes, there are more atoms in the system, but only 2837 of them are labeled
>> "CNT.' Well, I could share the files with you, of course, but you're
>> running the latest version, aren't you? :)
>>
>>
> As you might expect, yes.
>
> Do the atom numbers of the CNT start from 1, or is there something else
> listed before it in the coordinates and topology? If that's the case,
> making a matching .tpr via convert-tpr is the only option.
>
> -Justin
>
>
> On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 4/18/16 7:20 PM, Alex wrote:
>>>
>>> Justin,
>>>>
>>>> I understand what you're saying, but for the life of me I can't
>>>> understand
>>>> where this discrepancy is coming from, because the input coordinates
>>>> have
>>>> 2837 CNT atoms, and trjconv selector menu lists that number correctly.
>>>> Completely lost here. Are there any alternatives to output (in mdp) the
>>>> correct group?
>>>>
>>>>
>>>> Without access to your files, there's nothing else I can really tell
>>> you.
>>> Presumably there are more atoms in the system, yes? Your index group
>>> somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing the
>>> .tpr properly (use convert-tpr to output a matching .tpr that has only
>>> CNT
>>> and try again). I feel like there was an issue with this some time ago;
>>> 5.0.5 is considered old nowadays so the bug should have been fixed :)
>>>
>>> -Justin
>>>
>>>
>>> Alex
>>>
>>>>
>>>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 4/18/16 6:17 PM, Alex wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>>>
>>>>>> I've got a system that includes a group named "CNT" consisting of 2837
>>>>>> atoms. To save space, I am outputting (at a very high rate) a
>>>>>> compressed
>>>>>> trajectory that contains only that group. The GMX version is 5.0.5.
>>>>>> Here's
>>>>>> the relevant mdp excerpt:
>>>>>>
>>>>>>
>>>>>> nstxout = 10000
>>>>>> nstcomm = 1000
>>>>>> nstxout-compressed = 10
>>>>>> compressed-x-grps = CNT
>>>>>> nstvout = 1000
>>>>>> nstfout = 500
>>>>>> nstlog = 100
>>>>>> nstenergy = 500
>>>>>> nstlist = 20
>>>>>>
>>>>>> Upon trying to convert the compressed trajectory, after selecting the
>>>>>> appropriate group from the menu (CNT, 2837 atoms), I get:
>>>>>>
>>>>>> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb
>>>>>>
>>>>>> output:
>>>>>> -------------------------------------------------------
>>>>>> Program trjconv, VERSION 5.0.5
>>>>>> Source code file:
>>>>>>
>>>>>> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c,
>>>>>> line: 1330
>>>>>>
>>>>>> Fatal error:
>>>>>> Index[2645] 2838 is larger than the number of atoms in the
>>>>>> trajectory file (2837). There is a mismatch in the contents
>>>>>> of your -f, -s and/or -n files.
>>>>>> For more information and tips for troubleshooting, please check the
>>>>>> GROMACS
>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>>
>>>>>> Where's this single-atom discrepancy coming from? Any suggestions?
>>>>>>
>>>>>>
>>>>>> Whatever you selected as output contains more atoms than are in the
>>>>>>
>>>>> trajectory. Note that it's not necessarily a single-atom discrepancy,
>>>>> it's
>>>>> just that the fatal error is triggered as soon as an index that is out
>>>>> of
>>>>> range is identified. You're only outputting CNT, and presumably the
>>>>> .tpr
>>>>> contains more atoms, so the selection you're making can only be CNT or
>>>>> some
>>>>> subset of those atoms.
>>>>>
>>>>> -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
>>>>>
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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
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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