Dear Francois,
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?
Urszula
________________________________________
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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Received on Wed Nov 02 2011 - 05:30:04 PDT
