[gmx-users] trjconv index mismatch
Alex
nedomacho at gmail.com
Tue Apr 19 01:47:56 CEST 2016
You, my friend, are a genius. All worked, thanks tons.
Alex
On Mon, Apr 18, 2016 at 5:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/18/16 7:39 PM, Alex wrote:
>
>> 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?
>>
>>
> You need to make:
>
> 1. New .tpr with no restraints
> 2. Subset .tpr with just the CNT
>
>
> -Justin
>
>
>>
>> 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
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
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>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> 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!
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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
>>>
>>> * Please search the archive at
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>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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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
>
> * Please search the archive at
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> posting!
>
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>
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