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[modeller_usage] Re: Adding water molecules as ligands (minor corrections); modeller_usage Digest, Vol 5, Issue 3

Title: Re: Adding water molecules as ligands (minor corrections); modeller_usage Digest, Vol 5, Issue 3
Please note the corrections below:

Best regards,

Walid
>
> Today's Topics:
>
>    1. Re: modeller_usage Digest, Vol 5, Issue 2 (Mohsen, Al-Walid)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 03 Jan 2006 11:09:35 -0500
> From: "Mohsen, Al-Walid" <>
> Subject: [modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 2
> To: <>
> Message-ID: <BFE00BEF.2014%>
> Content-Type: text/plain; charset="US-ASCII"
>
> If you're only trying to include 3 water molecules that you know are
> important, try the following:
>
> 1- Edit the pdb file of your template to only include these specific ones,
> i.e, delete all other water molecules. Number these three water molecules 515
> 516, and 517.
> 2- Edit your .top file deleting the WATER_IO = on command and leave the
>     HETATM_IO = on command.
> 3- I usually use .pir and not .ali but this may still be applicable. Edit
> your .ali file as follows:
>     (a)   Change the second line in the paragraph so it will be:
>           structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00
>
>     (b)   Remove the /w* at the end of the molecule from both template and
> your sequence (model) lines.
>     (c)   After the last residue in the template, add XXX* that would
> correspond to the 3 water molecules in the pdb file.
>     (d)   After the last residue in the Sequence (model) lines add   ...*
>     (e)   Make sure that the XXX* in the template and the model ...* align exactly
> right. It seems you will not have a problem with this since the alignment is
> rather simple.
>     (f)   Change the second line in the template paragraph to:
>           sequence:CcHh1:1 : :523 : :unknown:unknown:-1.00:-1.00
>     
> I might be wrong but it seems like Modeler is confused about what is "w".
>
> I hope it works!!
>
> Best regards,
>
> Walid Mohsen
>
> Al-Walid A. Mohsen, Ph.D.
> Research Assistant Professor
> Department of Pediatrics
> School of Medicine
> University of Pittsburgh
> 3460 Fifth Ave, Rangos 2113
> Pittsburgh,  PA 15213
> U.S.A.
> Phone: (412) 692-7928
>
>
>
>> From: <>
>> Reply-To: <>
>> Date: Tue, 3 Jan 2006 02:52:59 -0800
>> To: <>
>> Subject: modeller_usage Digest, Vol 5, Issue 2
>>
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>>
>> Today's Topics:
>>
>>    1. modelling with ligands again! mainly water issues (jo hanna)
>>    2. Modelling with ligands - Not Working! (Joanne Hanna)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 3 Jan 2006 10:21:12 +0000
>> From: jo hanna <>
>> Subject: [modeller_usage] modelling with ligands again! mainly water
>> issues
>> To:
>> Message-ID:
>> <>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello again
>>
>> In follow up to my own question I have found that the issue only really
>> occurs when i try to include the water, either with the other ligand or even
>> without (after re ordering of the pdb file) Does the water in the pdb file
>> have to have H atoms attached or is a crystallographic O sufficient?
>>
>> My log with the hetatms only no water, is:
>> delete__442E> One or more atoms absent from MODEL:  O: 522: C: 522: N: 523:
>> CA: 523:
>> delete__442E> One or more atoms absent from MODEL:  O: 523: C: 523: N: 524:
>> CA: 524:
>> delete__443_> Restraints marked for deletion were removed.
>>               Total number of restraints before, now:    51172    47475
>>
>> which still shows these atoms absent errors which i don't understand.
>>
>> When adding just the water and no other ligand my top and aln files are
>> appended and my log error is an out of bounds as before. SO it aapears that
>> the water is the problem, I have also tried in my log file with only the
>> water changing the line SET HETATM_IO = on, WATER_IO = on to just SET
>> WATER_IO = on but this maks no difference.
>>
>> delete__442E> One or more atoms absent from MODEL:  O: 522: C: 522: N: 523:
>> CA: 523:
>> delete__443_> Restraints marked for deletion were removed.
>>               Total number of restraints before, now:    48782    45085
>> nselat__596E> Atom index is out of range (iatm,natm):     4009     4008
>> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
>>
>> TOP
>> INCLUDE
>> SET ALNFILE = 'CcHh1-Bamu.ali'
>> SET KNOWNS = 'Bamu'
>> SET SEQUENCE = 'CcHh1'
>> SET STARTING_MODEL = 1
>> SET ENDING_MODEL = 1
>> SET HETATM_IO = on, WATER_IO = on
>> CALL ROUTINE = 'model'\
>>
>> ALIGNMENT
>>> P1;Bamu
>> structureX:Bamu:1::515::undefined:undefined:-1.00:-1.00
>> GTHEEEQYLFAVNNTKAEYPRDKTIHQLFEEQVSKRPNNVAIVCENEQLTYHELNVKANQLARIFIEKGIGKDTL
>> VGIMMEKSIDLFIGILAVLKAGGAYVPIDIEYPKERIQYILDDSQARMLLTQKHLVHLIHNIQFNGQVEIFEEDT
>> IKIREGTNLHVPSKSTDLAYVIYTSGTTGNPKGTMLEHKGISNLKVFFEN-SLNVTEKDRIGQFASISFDASVWE
>> MFMALLTGASLYIILKDTINDFVKFEQYINQKEITVITLPPTYVVHL-----DPERILSIQTLITAGSATSPSLV
>> NKWKE--KVTYINAYGPTETTICATTWVATKETIGHSVPIGAPIQNTQIYIVDENLQLKSVGEAGELCIGGEGLA
>> RGYWKRPELTSQKFVDNPFVP-GEKLYKTGDQARWLSDGNIEYLGRIDNQVKIRGHRVELEEVESILLKHMYISE
>> TAVSVHKDHQEQPYLCAYFVSE---KHIPLEQLRQFSSEELPTYMIPSYFIQLDKMPLTSNGKIDRKQLPEPDLT
>> F/w*
>>
>>> P1;CcHh1
>> sequence:CcHh1:1::523::::0.00: 0.00
>> GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV
>> VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR
>> FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE
>> IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY
>> ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG
>> RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH
>> TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP
>> A/w*
>>
>> Sorry to post so many mails, I'm really struggling to figure this out!
>>
>> Jo
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://salilab.org/archives/modeller_usage/attachments/20060103/748155d8/atta>> c
>> hment.html
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 02 Jan 2006 21:49:33 +0000
>> From: "Joanne Hanna" <>
>> Subject: [modeller_usage] Modelling with ligands - Not Working!
>> To: <>
>> Message-ID: <>
>> Content-Type: text/plain; charset=US-ASCII
>>
>> Hello
>>
>> I have been using modeller for some time now but have only recenetly
>> tried to produce a model including ligands and I am having some
>> difficulties (I am using 7v7, and therefore the top scripts). I would
>> really appreciate some help or advice!
>>
>> The tutorial suggests that in order to include ligands in the modelling
>> process:
>>
>> Manually alter alignment to take account of 'block' (in this case AMP,
>> Mg and one H2O).
>> e.g. i have added /..w* at end of template and target in *.ali alignment
>> file
>>
>> Then use this alignment, together with a pdb containing the
>> ligands/cofactors/water to produce a model containing the ligands.
>> including the hetatm and water in the top file.
>>
>> This doesn't seem to work for me however. I have to change the number of
>> residues in the alignment file from 514 to 517 to take account of the 3
>> 'ligands' and when i run my model.top scripts (see below) i get the
>> following failure:
>>
>> Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
>>
>> ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
>> ----------------------------------------------
>>     134     1  134   138      G     E    8.407
>> END OF TABLE
>>
>> delete__442E> One or more atoms absent from MODEL:  O: 522: C: 522: N:
>> 523: CA: 523:
>> delete__442E> One or more atoms absent from MODEL:  O: 523: C: 523: N:
>> 524: CA: 524:
>> delete__442E> One or more atoms absent from MODEL:  O: 524: C: 524: N:
>> 525: CA: 525:
>> delete__443_> Restraints marked for deletion were removed.
>>               Total number of restraints before, now:    51247    47550
>> nselat__596E> Atom index is out of range (iatm,natm):     4033     4032
>> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
>>
>> I know that my alignment is not brilliant in the region 134-138 but it
>> is the other errors that are puzzling me. I particularly don't
>> understand the range error as i have 4142 atoms in my pdb file. And
>> there are no atoms missing from my pdb file as I have rebuilt all
>> missing atoms from the inital pdb using the modeller loop routine.
>>
>> Can anyone suggest how to fix this, or indeed tell me if the procedure
>> that i have gone through is correct?In addition to this in the alignment
>> file the -1.00:-1.00 part, is this correct?
>>
>> Many thanks in advance for any help/suggestions!
>>
>> Jo
>>
>> alignment file (after modeification of /..w and 517 residues in
>> structure):
>>> P1;Bamu
>> structureX:Bamu:   1 : : 517 : :undefined:undefined:-1.00:-1.00
>> GTHEEEQYLFAVNNTKAEYPRDKTIHQLFEEQVSKRPNNVAIVCENEQLTYHELNVKANQLARIFIEKGIGKDTL
>> VGIMMEKSIDLFIGILAVLKAGGAYVPIDIEYPKERIQYILDDSQARMLLTQKHLVHLIHNIQFNGQVEIFEEDT
>> IKIREGTNLHVPSKSTDLAYVIYTSGTTGNPKGTMLEHKGISNLKVFFEN-SLNVTEKDRIGQFASISFDASVWE
>> MFMALLTGASLYIILKDTINDFVKFEQYINQKEITVITLPPTYVVHL-----DPERILSIQTLITAGSATSPSLV
>> NKWKE--KVTYINAYGPTETTICATTWVATKETIGHSVPIGAPIQNTQIYIVDENLQLKSVGEAGELCIGGEGLA
>> RGYWKRPELTSQKFVDNPFVP-GEKLYKTGDQARWLSDGNIEYLGRIDNQVKIRGHRVELEEVESILLKHMYISE
>> TAVSVHKDHQEQPYLCAYFVSE---KHIPLEQLRQFSSEELPTYMIPSYFIQLDKMPLTSNGKIDRKQLPEPDLT
>> F/..w*
>>
>>> P1;CcHh1
>> sequence:CcHh1:     : :     : :::-1.00:-1.00
>> GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV
>> VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR
>> FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE
>> IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY
>> ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG
>> RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH
>> TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP
>> A/..w*
>>
>> top script:
>>
>> INCLUDE
>> SET ALNFILE = 'CcHh1-Bamu.ali'
>> SET KNOWNS = 'Bamu'
>> SET SEQUENCE = 'CcHh1'
>> SET STARTING_MODEL = 1
>> SET ENDING_MODEL = 1
>> SET HETATM_IO = ON, WATER_IO = ON
>> CALL ROUTINE = 'model'
>>
>> Joanne Hanna
>> Department of Chemistry
>> University of Warwick
>> Coventry
>> CV4 7AL
>>
>>
>>
>>
>> ------------------------------
>>
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>>
>> End of modeller_usage Digest, Vol 5, Issue 2
>> ********************************************
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