Dear Yeping Sun,
> It looks like you did not use Ante_R.E.D. 2.0; chemical equivalencing
> is not correctly performed: The charges are all but correct when one
> wishes to use them in MD simulation.
> I would use R.E.D. Server; first Ante_R.E.D. 2.0 and then R.E.D. III.x
> or R.E.D. IV.
>
> I let you know what we get with R.E.D. Python...
See the R.E.D. Python job; your data at:
http://q4mdfft:q4mdfft2013.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/
login:cluster -> q4mdfft:q4mdfft2013
I did not know what you wanted; so I generated FF libs for (i) the
whole molecule and (ii) a putative molecular fragment at the CH3CO-NHR
position:
See:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Project.config
See a .jpg image with atom typing for the whole molecule:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/molecule.jpg
& its corresponding fragment:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/fragment.jpg
See the corresponding RESP inputs for the whole molecule:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/input1_m1
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/input2_m1
& its corresponding fragment:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/input1_m1.sm
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/input2_m1.sm
Charges are corrected for rounding off errors:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-charge.log
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-charge.sm.log
The FF libs in the mol3 file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-o1.mol2
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-o1-sm1.mol2
the mol3 file format is interesting mainly for the fragment where the
N2 atom is defined has a 'head'...
please, have a look at the charge values (do not pay attention to the
polarizability values); the values, which are equivalent are forced to
be equivalent because the corresponding atoms are chemically
equivalent (this is defined in the RESP inputs). this is important for
MD simulations...
See the frcmod files:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Data-Default-Proj/frcmod.known
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Data-Default-Proj/frcmod.correspondence
-> empty
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown
-> 'CM-C -O2' is unknown; well, our algo. were not able to find a
correspondence; we will correct that; you could define that and add it
quite easily...
the corresponding leaprc file:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft
Data are kept 5 days on R.E.D. Server; see:
http://q4md-forcefieldtools.org/REDS/faq.php#11
I hope this helps.
regards, Francois
>> Thank you for your explanation. According to your instruction, I use
>> antechamber -i G39_H.pdb -fi pdb -o G39_H.mol2 -fo mol2 -c bcc
>> to produce the mol2 file, and then use
>> parmchk -i G39_H.mol2 -f mol2 -o frcmod
>> to produce the frcmod file. This time the G39_H.mole file seems to
>> have atom types in it. Next I use
>> tleap -s -f leap.in
>> the leap.in file is:
>> source leaprc.gaffsource leaprc.ff10leaprc.ff03.r1loadamberparams
>> frcmodMOL = loadmol2 G39_H.mol2comp = loadpdb
>> 3cl0_H274Y_N1_H_SG_noh.pdbbond comp.92.SG comp.417.SGbond
>> comp.124.SG comp.129.SGbond comp.183.SG comp.230.SGbond comp.232.SG
>> comp.237.SGbond comp.91.SG comp.417.SGbond comp.124.SG
>> comp.129.SGbond comp.183.SG comp.230.SGbond comp.232.SG
>> comp.237.SGbond comp.278.SG comp.291.SGbond comp.91.SG
>> comp.417.SGbond comp.280.SG comp.289.SGbond comp.318.SG
>> comp.336.SGbond comp.421.SG comp.447.SGsolvatebox comp TIP3PBOX
>> 10.0addions comp Na+ 0saveoff comp 3cl0.offsaveamberparm comp
>> 3cl0.prmtop 3cl0.inpcrdquit
>> But I still get the error message (please see leap.log);
>> Fatal: Atom .R<G39 469>.A<C1 1> does not have a type
>> ....................................................................................................
>> FATAL: Atom .R<G39 469>.A<N4 20> does not have a type.
>>
>> I suspect that leap convert the original numbering of the ligand,
>> G39, from 800 to 469, so I change the G39 numbering from 800 to 469
>> in the pdb file (3cl0_H274Y_N1_H_SG_noh.pdb) and save the new file
>> as 3cl0_H274Y_N1_H_SG_noh.pdb, and change the G39 numbering from 800
>> to 469 in the mol2 file and save the new mol2 file as
>> G39_H_mod.mol2, and change the input names of the pdb and mol2 files
>> in leap.in accordingly and save the new file as leap_mod.in.
>> However, I get new error message "Illegal CONECT record in pdb
>> file". Please see leap_mod.log)
>> The files including 3cl0_H274Y_N1_H_SG_noh.pdb,
>> 3cl0_H274Y_N1_H_SG_noh_mod.pdb, G39_H.pdb, G39_H.mol2, frcmod,
>> G39_H_mod.mol2, leap.in, leap_mod.in, leap.log, leap_mod.log are
>> included in the attachment.
>> Could you help me with it? Thank you!
>>
>> Sincerely,
>> Yeping Sun
>> ------------------------------------------------------------------????FyD<fyd.q4md-forcefieldtools.org>?????2013?6?28? 15:04????AMBER Mailing List<amber.ambermd.org>;????Re: [AMBER] FATAL: Atom XXX does not have a type Dear Yeping Sun,R.E.D. III.x or R.E.D. IV (Perl) does _not_ perform atom typing (R.E.D. Python does). You need to define the atom types in the mol2 file...Let's take an example in R.E.DD.B.http://q4md-forcefieldtools.org/REDDB/projects/W-1/The mol2 file:http://q4md-forcefieldtools.org/REDDB/projects/W-1/tripos1.mol2.<TRIPOS>ATOM 1 C1 1.352237 -0.856933 0.225852 C 1 DMSO -0.2897 **** 2 H11 1.336243 -1.843530 -0.221408 H 1 DMSO 0.1284 **** 3 H12 1.276947 -0.923392 1.304085 H 1 DMSO 0.1284 **** 4 H13 2.275139 -0.356278 -0.035153 H 1 DMSO 0.1284 **** 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177 **** 6 O3 -0.000040 1.405694 0.357557 O 1 DMSO -0.5085 **** 7 C4 -1.352189 -0.857006 0.225851 C 1 DMSO -0.2897 **** 8 H41 -2.275117 -0.356396 -0.035149 H 1 DMSO 0.1284
>> ****
>> 9
>> H42 -1.336143 -1.843599 -0.221415 H 1 DMSO 0.1284 **** 10 H43
>> -1.276895 -0.923466 1.304085 H 1 DMSO 0.1284 **** ^^^^^ ** here as
>> you can see the chemical elements have to be replaced by the atom
>> types; i.e. in this case:.<TRIPOS>ATOM 1 C1 1.352237 -0.856933
>> 0.225852 CT 1 DMSO -0.2897 **** 2 H11 1.336243 -1.843530 -0.221408
>> H1 1 DMSO 0.1284 **** 3 H12 1.276947 -0.923392 1.304085 H1 1 DMSO
>> 0.1284 **** 4 H13 2.275139 -0.356278 -0.035153 H1 1 DMSO 0.1284 ****
>> 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177 **** 6 O3
>> -0.000040 1.405694 0.357557 O 1 DMSO -0.5085 **** 7 C4 -1.352189
>> -0.857006 0.225851 CT 1 DMSO -0.2897 **** 8 H41 -2.275117 -0.356396
>> -0.035149 H1 1 DMSO 0.1284 **** 9 H42 -1.336143 -1.843599 -0.221415
>> H1 1 DMSO 0.1284 **** 10 H43 -1.276895 -0.923466 1.304085 H1 1 DMSO
>> 0.1284 ****You could do that using the 'set' command on the LEaP
>> program:See
>> http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.63See for
>> instance the LEaP script in R.E.DD.B.: http://q4md-forcefieldtool
>> s.org/REDDB/projects/W-46/script1.ff# tripos1.mol2set DMSO.1.C1 type
>> CTset DMSO.1.H11 type H1set DMSO.1.H12 type H1set DMSO.1.H13 type
>> H1# You might prefer to add your own FF atom types for S2 & O3set
>> DMSO.1.S2 type SXset DMSO.1.O3 type OXset DMSO.1.C4 type CTset
>> DMSO.1.H41 type H1set DMSO.1.H42 type H1set DMSO.1.H43 type H1or I
>> guess you can use Antechamber to load the mol2 file generated by
>> R.E.D. without atom types and output another mol2 file with atom
>> types...you could also send us your R.E.D. job as well (replacing
>> the .com gaussian input by .com.txt to avoid problems with mail
>> servers) so that we run the Re-fit mode of R.E.D. Python to generate
>> a mol3 file with residue connection (if needed), atom types, charges
>> corrected for rounding error errors with frcmod files, we can add
>> lone pairs and extra-points, united carbons, etc...if you used
>> R.E.D. Server just request a private assistance from the web site &
>> provide the PXXXX R.E.D. Server job name.See http://q4md-forcefieldtoo
>> ls.org/REDS/faq.php#5 we can take data from there & regenerate data
>> for you; see:http://q4md-forcefieldtools.org/REDS/faq.php#22regards,
>> Francois> I am trying to prepare the input files for amber
>> simulation on a > protein-ligand. The ligand is named G39 in the pdb
>> file. I used > R.E.D. server to generate the mol2 file
>> (Mol_m1-o1.mol2) and then > used parmchk to produce the frcmod
>> file. Next I tried to use tleap, > and the leap.in file is:> source
>> leaprc.gaffsource leaprc.ff10loadamberparams frcmodMOL = > loadmol2
>> Mol_m1-o1.mol2comp = loadpdb complex.pdbbond comp.92.SG >
>> comp.417.SGbond comp.124.SG comp.129.SGbond comp.183.SG >
>> comp.230.SGbond comp.232.SG comp.237.SGbond comp.91.SG >
>> comp.417.SGbond comp.124.SG comp.129.SGbond comp.183.SG >
>> comp.230.SGbond comp.232.SG comp.237.SGbond comp.278.SG >
>> comp.291.SGbond comp.91.SG comp.417.SGbond comp.280.SG >
>> comp.289.SGbond comp.318.SG comp.336.SGbond comp.421.SG >
>> comp.447.SGsolvatebox comp TIP3PBOX 10.0addions comp Na+ 0saveoff >
>> comp
>> 3cl0.offsaveamberparm comp 3cl0.prmtop 3cl0.inpcrdquit> > However,
>> when I run tleap -s -f leap.in, I get the follow output:> Loading
>> parameters: ./frcmodReading force field modification type > file
>> (frcmod)Reading title:remark goes hereLoading Mol2 file: >
>> ./Mol_m1-o1.mol2Reading MOLECULE named G39Loading PDB file: >
>> ./3cl0_H274Y_N1_H_SG_noh.pdbUnknown residue: CA number: 385 >
>> type: NonterminalUnknown residue: G39 number: 386 type: >
>> NonterminalCreated a new atom named: OXT within residue: .R<ILE >
>> 467>Creating new UNIT for residue: CA sequence: 468One sided >
>> connection. Residue: missing connect0 atom.Created a new atom >
>> named: CA within residue: .R<CA 468>Creating new UNIT for residue: >
>> G39 sequence: 469Created a new atom named: C1 within residue: .R<G39
>> > 469>Created a new atom named: O1A within residue: .R<G39
>> 469>Created > a new atom named: O1B within residue: .R<G39
>> 469>Created a new atom > named: C2 within residue: .R<G39
>> 469>Created a new atom named: C3 > with
>> in residue: .R<G39 469>Created a new atom named: C4 within >
>> residue: .R<G39 469>Created a new atom named: C5 within residue: >
>> .R<G39 469>Created a new atom> named: N5 within residue: .R<G39
>> 469>Created a new atom named: C10 > within residue: .R<G39
>> 469>Created a new atom named: O10 within > residue: .R<G39
>> 469>Created a new atom named: C11 within residue: > .R<G39
>> 469>Created a new atom named: C6 within residue: .R<G39 >
>> 469>Created a new atom named: C7 within residue: .R<G39 469>Created
>> > a new atom named: O7 within residue: .R<G39 469>Created a new atom
>> > named: C8 within residue: .R<G39 469>Created a new atom named: C9
>> > within residue: .R<G39 469>Created a new atom named: C81 within >
>> residue: .R<G39 469>Created a new atom named: C82 within residue: >
>> .R<G39 469>Created a new atom named: C91 within residue: .R<G39 >
>> 469>Created a new atom named: N4 within residue: .R<G39 469> total
>> > atoms in file: 3161 Leap added 3138 missing atoms according to >
>> residue templates: 3
>> 138 H / lone pairs The file contained 22 > atoms not in residue
>> templatesbond: Argument #1 is type String must > be of type:
>> [atom]usage: bond <atom1> <atom2> [order]bond: Argument > #1 is
>> type String must be of type: [atom]usage: bond <atom1> > <atom2>
>> [order]bond: Argument #1 is type String must be of type: >
>> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type
>> > String must be of type: [atom]usage: bond <atom1> <atom2> >
>> [order]bond: Argument #1 is type String must be of type: >
>> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type
>> > String must be of type: [atom]usage: bond <atom1> <atom2> >
>> [order]bond: Argument #1 is type String must be of type: >
>> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type
>> > String must be of type: [atom]usage: bond <atom1> <atom2> >
>> [order]bond: Argument #2 is type String must be of type: >
>> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #2 is type
>> > String must be of type: [atom]usage: bo
>> nd <atom1> <atom2> > [order] (using default radius 1.500000 for
>> OXT) (using default > radius 1.500000 for CA) (using default radius
>> 1.500000 for > C1) (using default radius 1.500000 for O1A) (using
>> default radius > 1.500> 000 for O1B) (using default radius 1.500000
>> for C2) (using default > radius 1.500000 for C3) (using default
>> radius 1.500000 for > C4) (using default radius 1.500000 for
>> C5) (using default radius > 1.500000 for N5) (using default radius
>> 1.500000 for C10) (using > default radius 1.500000 for O10) (using
>> default radius 1.500000 for > C11) (using default radius 1.500000
>> for C6) (using default radius > 1.500000 for C7) (using default
>> radius 1.500000 for O7) (using > default radius 1.500000 for
>> C8) (using default radius 1.500000 for > C9) (using default radius
>> 1.500000 for C81) (using default radius > 1.500000 for C82) (using
>> default radius 1.500000 for C91) (using > default radius 1.500000
>> for N4) Solute vdw bounding > box: 57.502 57.677
>> 61.240 Total bou
>> nding box for atom > centers: 77.502 77.677 81.240 Solvent unit >
>> box: 18.774 18.774 18.774 (using default radius
>> > 1.500000 for OXT) (using default radius 1.500000 for CA) (using >
>> default radius 1.500000 for C1) (using default r> adius 1.500000 for
>> O1A) (using default radius 1.500000 for > O1B) (using default radius
>> 1.500000 for C2) (using default radius > 1.500000 for C3) (using
>> default radius 1.500000 for C4) (using > default radius 1.500000 for
>> C5) (using default radius 1.500000 for > N5) (using default radius
>> 1.500000 for C10) (using default radius > 1.500000 for O10) (using
>> default radius 1.500000 for C11) (using > default radius 1.500000
>> for C6) (using default radius 1.500000 for > C7) (using default
>> radius 1.500000 for O7) (using default radius > 1.500000 for
>> C8) (using default radius 1.500000 for C9) (using > default radius
>> 1.500000 for C81) (using default radius 1.500000 for > C82) (using
>> default radius 1.500000 for C91) (using default radius > 1.50
>> 0000 for N4) Total vdw box size: 80.756 > 81.019
>> 84.432 angstroms. Volume: 552415.997 A^3 Mass > 274487.606 >
>> amu, Density > 0.825 g/cc (type - hence mass - of one or more
>> > atoms could not be found) Added 12722 residues.3 Na+ ions
>> required > to neutraliz> e.Using default radius 1.50 for ion
>> Na+Adding 3 counter ions to > "comp" using 1A gridUsed default
>> radius 1.50 for 22 atomsGrid > extends from solute vdw + 1.50 to
>> 7.50Resolution: 1.00 > Angstrom.grid build: 1 secSolvent
>> present: replacing closest with > ion when steric overlaps
>> occurCalculating grid > chargescharges: 9 sec(Replacing solvent
>> molecule)Placed Na+ in comp > at (-22.85, 22.75, 4.56).(No solvent
>> overlap)Placed Na+ in comp at > (19.11, -6.61, -17.97).(Replacing
>> solvent molecule)Placed Na+ in > comp at (5.85, 31.42, 8.49).Done
>> adding ions.Building > topology.Building atom parameters.Checking
>> Unit.FATAL: Atom .R<ILE > 467>.A<OXT 20> does not have a
>> type.FATAL: Atom .R<CA 46
>> 8>.A<CA 1> > does not have a type.FATAL: Atom .R<G39 469>.A<C1 1>
>> does not have > a type.FATAL: Atom .R<G39 469>.A<O1A 2> does not
>> have a > type.FATAL: Atom .R<G39 469>.A<O1B 3> does not have a
>> type.FATAL: > Atom .R<G39 469>.A<C2 4> does not have a type.FATAL:
>> Atom .R<G39 > 469>.A<C3 5> does not have a type.FA> TAL: Atom
>> .R<G39 469>.A<C4 6> does not have a type.FATAL: Atom > .R<G39
>> 469>.A<C5 7> does not have a type.FATAL: Atom .R<G39 > 469>.A<N5 8>
>> does not have a type.FATAL: Atom .R<G39 469>.A<C10 9> > does not
>> have a type.FATAL: Atom .R<G39 469>.A<O10 10> does not > have a
>> type.FATAL: Atom .R<G39 469>.A<C11 11> does not have a >
>> type.FATAL: Atom .R<G39 469>.A<C6 12> does not have a type.FATAL:
>> > Atom .R<G39 469>.A<C7 13> does not have a type.FATAL: Atom .R<G39
>> > 469>.A<O7 14> does not have a type.FATAL: Atom .R<G39 469>.A<C8
>> 15> > does not have a type.FATAL: Atom .R<G39 469>.A<C9 16> does
>> not have > a type.FATAL: Atom .R<G39 469>.A<C81 17> does not have a
>> > type.
>> FATAL: Atom .R<G39 469>.A<C82 18> does not have a type.FATAL: >
>> Atom .R<G39 469>.A<C91 19> does not have a type.FATAL: Atom .R<G39
>> > 469>.A<N4 20> does not have a type.Failed to generate >
>> parametersParameter file was not saved. Quit> The ligand,
>> G39, is numbered 800 in the original pdb file, but leap > seemed to
>> renumber it as 469. Except the difference in G39 > numbering, I
>> cannot find any other thing that cause the errors, > Could you help
>> me figure it out? Thanks in
>> advance._______________________________________________AMBER mailing
>> listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jul 02 2013 - 06:30:02 PDT
