Re: [AMBER] ظRe: ???Re: FATAL: Atom XXX does not have a type

From: Biao Ma <jackyma1981.gmail.com>
Date: Thu, 4 Jul 2013 12:12:09 +0900

Hi, Yeping,

login:cluster -> q4mdfft:q4mdfft2013
Is "cluster" the account and "q4mdfft:q4mdfft2013" the password? I have
tried this but failed. Could you explain it?

by my experiences, the acount is "q4mdfft", q4mdfft2013 may be the password.

Jacky
On Thu, Jul 4, 2013 at 12:03 PM, <sunyeping.aliyun.com> wrote:

> Dear professor Francois,
>
> I try to obtain the data you provide in this previous mail, but I still
> cannot login in any of the links you list, I don't understand the login
> method you mentioned in the mail:
>
> login:cluster -> q4mdfft:q4mdfft2013
> Is "cluster" the account and "q4mdfft:q4mdfft2013" the password? I have
> tried this but failed. Could you explain it?
>
> Regards,
>
> Yeping Sun
> ------------------------------------------------------------------ˣFyD<
> fyd.q4md-forcefieldtools.org>ڣ201372 21:00ռˣAMBER Mailing List<
> amber.ambermd.org>; ⣺Re: [AMBER] ???Re: FATAL: Atom XXX does not have a
> typeDear 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:q4mdfft2013I 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.configSeea .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.jpgSeethe 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_m1http://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.smhttp://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/input2_m1.smChargesare 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.loghttp://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-charge.sm.logTheFF libs in the mol3 file format:
> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.phphttp://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-o1.mol2http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Mol_m1/Mol_m1-o1-sm1.mol2themol3 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.knownhttp://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Data-Default-Proj/frcmod.correspondence->
> emptyhttp://
> 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.ff13q4mdfftDataare kept 5 days on R.E.D. Server; see:
> http://q4md-forcefieldtools.org/REDS/faq.php#11I 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.infile is:>> source leaprc.gaffsource
> leaprc.ff10leaprc.ff03.r1loadamberparams>> frcmodMOL = loadmol2
> G39_H.mol2comp = loadpdb>> 3cl0_H274Y_N1_H_SG_noh.pdbbond comp.92.SGcomp.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.SGcomp.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.SGcomp.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.SGcomp.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>>
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Received on Wed Jul 03 2013 - 20:30:02 PDT
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