Dear Ibrahim,
> I got the following file for capped Lys-Frupyr
> fragment. The RED server name P2909, but I recognized some files active and
> others are inactive. Also, I don' t know if these large number of files
> indicates the QM run is Ok.
You ran a big job and automatically generated FF libraries for the
N-term, C-term & central fragments + the corresponding dipeptide
according to the tutorial at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
Yes, a lot of files were generated:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909.html
this is normal you get lost ;-)
All the files generated by R.E.D. Server are described at:
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/listing-6mol.pdf
see page 5: you really need:
mm1-o1.FG2.mol2 Central fragment: Molecule 1 – conformation 1 (Fragment 2)
mm3-o1-FG.mol2 N-terminal fragment: Molecule 3 – conformation 1
mm5-o1-FG.mol2 C-terminal fragment: Molecule 5 – conformation 1
mm6-o1.mol2 Molecule 6 – conformation 1
& likely only:
mm1-o1.FG2.mol2 Central fragment: Molecule 1 – conformation 1 (Fragment 2)
The key P2N file is the first one of the six files:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Mol_red1.p2n
-> chemical equivalencing was generated by Ante_R.E.D. 2.0 -> all is ok:
http://q4md-forcefieldtools.org/REDS/news.php#2
REMARK Information automatically added by R.E.D. Server
REMARK INTRA-MCC 0.0000 | 1 2 3 4 5 6 | Remove
REMARK INTRA-MCC 0.0000 | 49 50 51 52 53 54 | Remove
-> this is to define the central fragment
REMARK INTER-MCC 0.0000 | 2 3 | 1 2 3 4 | 1 2 3 4 5 6 7 8
REMARK INTER-MCC 0.0000 | 4 5 | 1 2 3 4 | 47 48 49 50 51 52 53 54
-> this is to define the N-term & C-term fragments between molecules
2-3 & 4-5
the RRMS of the RESP fit with chemical equivalencing and all the
charge constraints:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_MM/output2_mm
ESP relative RMS (SQRT(chipot/ssvpot)) 0.03331
the RRMS of the 1st RESP stage without chemical equivalencing and
without the charge constraints:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_MM/stat-output-b_mm
ESP relative RMS (SQRT(chipot/ssvpot)) 0.02964
-> the difference 0.033-0.030 is pretty good...
You can also look at local/charge errors:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_MM/stat-RESP-FIT_mm
-> the errors are mainly observed for N-term & C-term fragments; this
is normal...
You decided to use 'pop=mk' for all your data; I think this is the
most simple; at least in a first approach:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_m1/JOB2-gau_m1-1-1.com
The key to finish to check your RESP charge derivation data:
do you like the conformation obtained after geometry optimization?:
See the java applet :
http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/javaappletpdb-1.html
The peptide backbone looks like to be in an extended conformation;
concerning the fructose part (
http://en.wikipedia.org/wiki/Fructose),
the conformation is not 4C1
(
http://web.inc.bme.hu/csonka/csg/glc/glc.htm); only you should know
what conformation you want for this fructose part: it should be close
to your experimental data or close to a choice you voluntary made!
I hope this helps...
regards, Francois
> On Fri, Feb 15, 2013 at 6:09 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Ibrahim,
>>
>> I continue my former email... In case you are interested in the mol3
>> file format you could have a look at the 'F-93' R.E.DD.B. project by
>> J. Sanders about peptide nucleic acid; this is an example where the
>> mol3 file format is used... This simplifies I think a lot the use of
>> force field libraries and the connections between fragments in the
>> LEaP program...
>> See http://q4md-forcefieldtools.org/REDDB/projects/F-93/
>>
>> regards, Francois
>>
>>
>> > thank you for helping. My R.E.D server name P2890 for Lys-Frupyr file.
>> Now
>> > I have the following problems: (1) how can ligate this dipeptide into my
>> > protein. of course, I need to assign atom types, (2) Can I use xleap and
>> > then add the fructose molecule to lysine residue in my protein manually,
>> > then select this residue and assign both atom types and add charges from
>> > P2890 file manually. The problem of later is, if I dismessed, I need to
>> > re-add atom types and charges in xleap. Please, any suggestions.
>>
>> > On Thu, Feb 14, 2013 at 9:00 AM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>> >
>> >> Dear Ibrahim,
>> >>
>> >> > I have built my dipeptide (Lysine-fructose). and I used RESP ESP
>> charge
>> >> > derived server to assign the atomic charges. Please, I used xleap to
>> add
>> >> > the same fructose moiety to the lysine residue in my protein and added
>> >> the
>> >> > charges and atom types to this fructose part manually. Of course, I
>> >> loaded
>> >> > both of leaprc.ff99SB and Glycam_06h. Now I get both top and crd files
>> >> but
>> >> > I do not know if these steps are Ok or no. please can you help me.
>> >>
>> >> This is difficult to help with so little information...
>> >>
>> >> -> I guess you generated a dipeptide for this Lysine-fructose and used
>> >> R.E.D. Server to generate a central fragment for this modified
>> >> dipeptide. May be you could provide in your email the 'PXXXX' R.E.D.
>> >> Server name so that we can more easily assist you by looking at your
>> >> R.E.D. Server job.
>> >>
>> >> To generate a central fragment for your modified dipeptide see:
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>> >>
>> >> To generate the N-term, C-term + central fragments manually, see:
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>> >>
>> >> To generate these 3 fragments automatically see:
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>> >>
>> >> key points here:
>> >> - is chemical equivalencing correctly defined in the P2N input file?
>> >> See http://q4md-forcefieldtools.org/REDS/news.php#2
>> >>
>> >> - what is/are the conformation(s) involved in charge derivation for
>> >> your dipeptide with this Lysine-fructose?
>> >>
>> >> - what is the algorithm used in MEP computation considering that you
>> >> use two different force fields which are based on different MEP
>> >> computation algorithm (Connolly surface vs CHELPG). To simplify all
>> >> that for this fructose-based central fragment of Lys, you might be
>> >> interested in an approach we develop for a-1,4 Glc oligomers:
>> >> see http://www.ncbi.nlm.nih.gov/pubmed/21792425 : the main idea in
>> >> this paper is to provide a highly consistent approach for force field
>> >> development for glycopeptides; however only tested for a-1,4 Glc based
>> >> oligomers. this means that if you decide to follow this approach you
>> >> will have to validate it (in all the cases you always have to validate
>> >> your approach; so no difference...)
>> >>
>> >> -> then at the end R.E.D. Server/R.E.D. IV provides a mol2 file or a
>> >> series of mol2 files that you have to load in LEaP. Here you need to
>> >> decide which force field(s) you plan to use and define the
>> >> corresponding atom types. Personally I always add these atom types
>> >> manually because I want to control my choices.
>> >>
>> >> -> finally you load all the FF libs, define the head/tails (to connect
>> >> them where they should be connected) in the LEaP program and generate
>> >> the prmtop/prmcrd files; if force field parameters are missing LEaP
>> >> will generate errors/the listing of these missing parameters; this
>> >> means you have to generate a frcmod file; once again I always generate
>> >> this frcmod file by hand to control my choices. See for instance:
>> >>
>> >> the R.E.DD.B. project in relation with the publication above
>> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/
>> >>
>> >> the definition of head/tail and FF atom types
>> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
>> >>
>> >> the frcmod file
>> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script3.ff
>> >>
>> >> I hope this helps...
>> >>
>> >> regards, Francois
>> >>
>> >>
>> >> > On Thu, Jan 24, 2013 at 9:51 AM, FyD <fyd.q4md-forcefieldtools.org>
>> >> wrote:
>> >> >
>> >> >> Dear Ibrahim,
>> >> >>
>> >> >> > I am trying to simulate the Schiff base for my protein in which
>> >> >> > lysine is binding the fructose molecule through a covalent bond
>> NZ-C1
>> >> of
>> >> >> > fructose. Can I use xleap to build this structure and how. What I
>> >> have in
>> >> >> > my hand that I should separate lysine residue from the protein and
>> >> attach
>> >> >> > it to fructose and then re-ligate, is it correct. I do not know how
>> >> can
>> >> >> > xleap can do.
>> >> >>
>> >> >> If I understand you you are interested in constructing a new residue
>> >> >> i.e. a L-lysine connected to D-fructose through an imine bond.
>> >> >>
>> >> >> You can use R.E.D. and/or R.E.D. Server for this work; and you can
>> >> >> directly build a new central fragment for this new Lysine residue.
>> >> >> See for instance:
>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
>> >> >> &
>> >> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>> >> >> vs
>> >> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>> >> >>
>> >> >> You could also consider splitting this 'lys-fructose' residue into
>> two
>> >> >> building blocks. You can find examples of such an approach in
>> R.E.DD.B.
>> >> >> See for instance in the sugar domain:
>> >> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/
>> >> >> http://q4md-forcefieldtools.org/REDDB/projects/F-72/
>> >> >> http://q4md-forcefieldtools.org/REDDB/projects/F-71/
>> >> >>
>> >> >> R.E.D. uses the P2N file format as input described at:
>> >> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
>> >> >> & generates FF library in the mol2 file format described at:
>> >> >> http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
>> >> >> This mol2 file format is directly usable in the LEaP prgram as
>> described
>> >> >> at:
>> >> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
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Received on Sun Feb 17 2013 - 05:00:03 PST
