Dear amber users,
I have a mol2 its a peptide (see attachment), I can also have it as a pdb file
but I got the same errors,
after loading to the xleap/tleap I am getting errors:
Checking 'x'....
WARNING: There is a bond of 5.692649 angstroms between:
------- .R<GLY 4>.A<C 6> and .R<PHE 5>.A<N 1>
WARNING: There is a bond of 6.860270 angstroms between:
------- .R<PHE 5>.A<C 19> and .R<PHE 5>.A<O 20>
WARNING: There is a bond of 6.814960 angstroms between:
------- .R<PHE 5>.A<C 19> and .R<LYS 6>.A<N 1>
WARNING: There is a bond of 4.824091 angstroms between:
------- .R<PHE 5>.A<CA 3> and .R<PHE 5>.A<C 19>
WARNING: There is a bond of 4.122393 angstroms between:
------- .R<PHE 5>.A<N 1> and .R<PHE 5>.A<H 2>
WARNING: There is a bond of 3.904530 angstroms between:
------- .R<PHE 5>.A<N 1> and .R<PHE 5>.A<CA 3>
WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
FATAL: Atom .R<PHE 5>.A<S 21> does not have a type.
FATAL: Atom .R<PHE 5>.A<HC 22> does not have a type.
FATAL: Atom .R<CLYS 12>.A<HC 24> does not have a type.
Warning: Close contact of 0.715937 angstroms between .R<PHE 5>.A<C 19> and .R<PHE 5>.A<CZ 13>
Warning: Close contact of 0.759931 angstroms between .R<PHE 5>.A<C 19> and .R<PHE 5>.A<CE1 11>
Warning: Close contact of 1.080065 angstroms between .R<PHE 5>.A<C 19> and .R<PHE 5>.A<HC 22>
Warning: Close contact of 1.341952 angstroms between .R<PHE 5>.A<HE2 16> and .R<PHE 5>.A<S 21>
Warning: Close contact of 0.523849 angstroms between .R<PHE 5>.A<CE2 15> and .R<PHE 5>.A<S 21>
Warning: Close contact of 1.251699 angstroms between .R<PHE 5>.A<HZ 14> and .R<PHE 5>.A<HC 22>
Warning: Close contact of 1.273293 angstroms between .R<PHE 5>.A<CZ 13> and .R<PHE 5>.A<S 21>
Warning: Close contact of 1.102773 angstroms between .R<PHE 5>.A<CZ 13> and .R<PHE 5>.A<HC 22>
Warning: Close contact of 1.269939 angstroms between .R<PHE 5>.A<HE1 12> and .R<PHE 5>.A<HC 22>
Warning: Close contact of 1.263048 angstroms between .R<PHE 5>.A<CE1 11> and .R<PHE 5>.A<N 1>
Warning: Close contact of 1.114439 angstroms between .R<PHE 5>.A<CE1 11> and .R<PHE 5>.A<HC 22>
Warning: Close contact of 1.351492 angstroms between .R<PHE 5>.A<HD1 10> and .R<PHE 5>.A<N 1>
Warning: Close contact of 0.382734 angstroms between .R<PHE 5>.A<CD1 9> and .R<PHE 5>.A<N 1>
Warning: Close contact of 1.409192 angstroms between .R<PHE 5>.A<CG 8> and .R<PHE 5>.A<N 1>
Warning: Close contact of 0.177387 angstroms between .R<CLYS 12>.A<OXT 23> and .R<CLYS 12>.A<HC 24>
Warning: Close contact of 1.080436 angstroms between .R<CLYS 12>.A<C 21> and .R<CLYS 12>.A<HC 24>
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 3 Warnings: 23
after editing the molecule is not the same, some bonds are broken and new bonds appeared
I have no idea what I could do and how to convert it properly?
I need to have an prmtop and incrd files for MD simulations,
Could anyone help me with this problem ?
thank you in advance
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Mittwoch, 2. November 2011 13:40
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides
Urszula,
> Thank you very much,that was very helpful.
> I was wondering about one more thing, I have just checked that
> when I removed
> all H atoms from pep1.pdb the amber does not have problem with that
> at least with this peptide ...
> would that be also correct?
Once you have loaded the FF libraries in LEaP, the later will add all
the missing atoms in the PDB file (for instance in your case if you
remove the hydrogens from the PDB file) based on the atom/residue
names present in the FF libraries. Obviously, a residue name match is
required between the PDB file and the FF libs...
regards, Francois
______________________________________
> Von: FyD [fyd.q4md-forcefieldtools.org]
> Gesendet: Mittwoch, 2. November 2011 09:10
> An: AMBER Mailing List
> Cc: q4md-fft Mailing list
> Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides
>
> Dear Urszula,
>
> - I used R.E.D. Server as defined .
> http://q4md-forcefieldtools.org/REDS/faq.php#21
> - See also the time the data are conserved on the R.E.D. Server hard
> drives when using the public account:
> http://q4md-forcefieldtools.org/REDS/faq.php#11
>
>
> -1- I used the conformation available in the PDB file you sent me to
> build a PDB file for ACE-LYA using a text editor & the xLEaP program:
> ATOM 1 CM ACE 1 16.356 -1.665 -37.543 35.99 35.99
> C
> ATOM 2 HM1 ACE 1 15.885 -1.580 -36.564 35.99 35.99
> H
> ATOM 3 HM2 ACE 1 17.338 -1.843 -37.477 1.00 0.00
> H
> ATOM 4 HM3 ACE 1 16.202 -0.856 -38.110 1.00 0.00
> H
> ATOM 5 C ACE 1 15.654 -2.882 -38.181 35.89 35.89
> C
> ATOM 6 O ACE 1 16.131 -4.011 -38.038 35.89 35.89
> O
> ATOM 7 N LYA 2 14.524 -2.637 -38.853 35.77 35.77
> N
> ATOM 8 H LYA 2 14.161 -1.695 -38.830 35.77 35.77
> H
> ATOM 9 CA LYA 2 13.767 -3.645 -39.628 35.58 35.58
> C
> ATOM 10 HA LYA 2 12.818 -3.158 -39.851 35.58 35.58
> H
> ATOM 11 CB LYA 2 14.480 -4.000 -40.949 35.44 35.44
> C
> ATOM 12 HB2 LYA 2 13.855 -4.713 -41.487 35.44 35.44
> H
> ATOM 13 HB3 LYA 2 15.433 -4.467 -40.701 35.44 35.44
> H
> ATOM 14 CG LYA 2 14.762 -2.816 -41.886 34.96 34.96
> C
> ATOM 15 HG2 LYA 2 15.533 -3.112 -42.598 34.96 34.96
> H
> ATOM 16 HG3 LYA 2 15.121 -1.978 -41.289 34.96 34.96
> H
> ATOM 17 CD LYA 2 13.527 -2.365 -42.665 34.65 34.65
> C
> ATOM 18 HD2 LYA 2 12.852 -3.214 -42.773 34.65 34.65
> H
> ATOM 19 HD3 LYA 2 13.841 -2.022 -43.651 34.65 34.65
> H
> ATOM 20 CE LYA 2 12.781 -1.230 -41.964 34.30 34.30
> C
> ATOM 21 HE2 LYA 2 13.463 -0.391 -41.826 34.30 34.30
> H
> ATOM 22 HE3 LYA 2 12.436 -1.581 -40.991 34.30 34.30
> H
> ATOM 23 NZ LYA 2 11.604 -0.771 -42.757 33.47 33.47
> N
> ATOM 24 HZ1 LYA 2 11.914 -0.443 -43.661 33.47 33.47
> H
> ATOM 25 HZ2 LYA 2 11.140 -0.019 -42.267 33.47 33.47
> H
> ATOM 26 HZ3 LYA 2 10.961 -1.540 -42.880 33.47 33.47
> H
> ATOM 27 C LYA 2 13.407 -4.915 -38.854 35.61 35.61
> C
> ATOM 28 O LYA 2 12.511 -5.663 -39.258 35.61 35.61
> O
> ATOM 29 HC LYA 2 13.941 -5.159 -37.947 35.61 35.61
> H
> END
>
>
> -2- I ran R.E.D. Server/Ante_R.E.D. 2.0 to generate a P2N file:
> See
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFsw7ItTLcADFn6byADF0HbcBADFBNTvKqqd5j0/P4231.html
> & the Java applet for the P2N file generated:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFsw7ItTLcADFn6byADF0HbcBADFBNTvKqqd5j0/P4231/javaappletp2n-1.html
>
>
> -3- I modified the P2N file to create the right total charge value
> (+1), to add a quick title and added a INTRA-MCC keyword to defined
> the terminal fragment to be designed as defined .
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15 (except
> that in your case a single INTRA-MCC keyword is used)
>
>
> -4- I ran R.E.D. Server/R.E.D. IV to derive charges and generate the
> FF library for the molecular fragment LYA. See
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232.html
> the P2N file modified in the step -3-
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232/Mol_red1.p2n
> the charge fit for the molecular fragment:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232/Data-R.E.D.Server/input1_m1.sm
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232/Data-R.E.D.Server/input2_m1.sm
> & the molecular fragment "LYA" in the Java applet: NHCHRCHO R=(CH2)4NH3(+)
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232/javaappletmol2-2.html
>
>
> -5- What next?
> - re-do this job with another input conformation (I do not like the
> conformation obtained after geom.optimization in this case) or a set
> of conformations
> - add the FF atom types (I did it for you; please upload this file
> separately; it is NOT present in the archive file)
> See
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232/Data-R.E.D.Server/Mol_m1-o1-sm-withFFAtomTypes.mol2
> (the tricks are to differentiate the H1, HC and HP atom types and
> define an atom type for this aldehyde hydrogen).
> - may be create a frcmod file for this aldehyde function if you use
> parm99.dat
>
> All that took me 5 minutes to set up in R.E.D. Server; I ran the job
> yesterday evening and got the data this morning... The R.E.D.
> server/R.E.D. IV job took around 2 hours when using 8 cores and the
> Firefly QC program:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFLkHVjZQOADFRodSh42PUtADFSOxlSGS5s80/P4232/R.E.D.-IV-5356.master0.q4md-forcefieldtools.org.log
>
> regards, Francois
>
>
> Quoting Urszula Uciechowska <urszula.uchiechowska.chem.umu.se>:
>
>> I am quite new to this, how to create a library for this?
>> Could please help me,
>> Urszula
>> ________________________________________
>> Von: FyD [fyd.q4md-forcefieldtools.org]
>> Gesendet: Dienstag, 1. November 2011 15:11
>> An: AMBER Mailing List
>> Betreff: Re: [AMBER] parameters for anchor-modified glycopeptides
>>
>> Urszula,
>>
>>> My problem is that AMBER is not handling that ( ff99SB), there is
>>> not sugar unit right now,
>>>
>>> when I am loading f.ex pep1.pdb to the tleap i am getting:
>>>
>>> Checking 'x'....
>>> WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
>>
>> -> A warning not a big deal ;-)
>>
>>> FATAL: Atom .R<CLYS 12>.A<HC 24> does not have a type.
>>
>> Yes this is the open valency I told you; LEaP reports a CLYS
>> residue... that has an aldehyde function instead of a carboxylate one;
>> you simply need to modify the C-terminal residue according to the FF
>> lib you are going to load in LEaP; in your case I guess you want to
>> use CLYS... or you need to create a new FF library for this
>> alpha-amino-...aldehyde ;-)
>>
>> regards, Francois
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- application/octet-stream attachment: pep4.mol2
Received on Thu Nov 03 2011 - 05:30:04 PDT
