Dear Yeping Sun,
> Based on the files you generated by R.E.D. Phython I set up a
> leap.in script and run tleap:
>
> tleap -s -f leap.in
>
> Unfortunately many errors occurred although the prmcrd and prmtop
> files was generated (please the leap.log). Could you check it for
> me? All relevent files are in the attachment.
it looks like you need to be more careful:
loadamberparams frcmod_unknown
-> is it the correct syntax?
See
http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.41
-> is it useful to do that considering that the FF constant and
equilibrium value is not even provided
bond mol.124.mol.129.SG
-> what does it mean?
run 'tleap -f script' once
if it does not work -> read the log file generated
before rerunning 'tleap -f script' be sure to rename the log file so
that you will always have a clean log...
do you need to load gaff?
regards, Francois
> ------------------------------------------------------------------????FyD<fyd.q4md-forcefieldtools.org>?????2013?7?4? 23:22????AMBER Mailing List<amber.ambermd.org>;????Re: [AMBER] Re?Re: FATAL: Atom XXX does not have a type Yeping Sun,> 1) you gave two frcmod files: frcmod.known and frcmod.unknow. You > assume I could easily define the unknow part (CM-CO2), but I don't > know how to define it. And can I use the two frcmod files directly > in leap to generate prmtop inpcrd files? What is correct format for > loading the two frcmod files?See the leaprc file generated in R.E.D. Python: Data-Default-Proj/leaprc.ff13q4mdfftfrcmod1 = loadAmberParams ./frcmod.knownfrcmod2 = loadAmberParams ./frcmod.correspondence# frcmod3 = loadAmberParams ./frcmod.unknownto generate the prmtop/prmcrd(inpcrd) files; just see the command that is commented in the leaprc file:saveAmberParm m1 m1.parm7 m1.rst7 (which is 'vmd' oriented)or if you prefer:saveAmberParm m1 prmtop inpcrd> 2) How can I know which parts of an organic molecule are known and > which parts are unknown? one FF parameter is missing; just provide it as it follows:FF constant Equilibrium value> 3?How was the leaprc file produced? In the leaprc file, there are > two files which you didn't mention previously. They > are ./frcmod.correspondence and ../Mol_m1/Mol_m1-o1-sm1.mol2. What > are they and where can I find them?R.E.D. Python dynamically generates the 3 frcmod files and the leaprc files as function of the atom types found and FF library generated.In your case you just need: Mol_m1/Mol_m1-o1.mol2(and not Mol_m1/Mol_m1-o1-sm1.mol2 which is a molecular fragment)regards, Francois> ------------------------------------------------------------------????FyD<fyd.q4md-forcefieldtools.org>?????2013?7?2? 23:00????AMBER Mailing List<amber.ambermd.org>;????Re: [AMBER] FATAL: Atom XXX does not have a typeYeping Sun,I checked P5493. I think you could
> use:http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/
> molecule.jpgThe 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_m1Charges 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.logThe FF lib 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.mol2See the frcmod > files:http://c> luster.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.unknown-> 'CM-C -O2' is unknown; well, our algo. were not able to find acorrespondence; we will correct
> tha
> t; you could define that and add itquite easily...The corresponding
> leaprc
> file:http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfftjust use 'm0'...The only differences in charge values between 'your' data and 'mine' should be related to molecular orientations; i.e. charge differences lower than .07 e.regards, Francois> I have used R.E.D. Server, and get the mol2 file. The job ID is > P5493. Please see the attachment. As you mentioned in the previous > mail that the mol2 file produced by R.E.D. Server doesn't has atom > type information, and you can help to produce a mol3 file > w> hich have > neccessary information needed by leap. Could you do > these for me? > > ------------------------------------------------------------------????FyD<fyd.q4md-forcefieldtools.org>?????2013?7?2? 21:00????AMBER Mailing List<amber.ambermd.org>;????Re: [AMBER] ???Re: FATAL: Atom XXX does not have a typeDear Yeping Sun,> It
> loo
> ks 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.configSee a .jpg image > with atom > typin> g 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.jpgSee the
> co
> rresponding 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.smCharges 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.loghtt> p://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF3-A-Yeping-Sun/Data-R.E.D.Server/> Mol_m1/Mol_m1-charge.sm.logThe FF 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.mol2the 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.knownhttp://cluster.q4md-f> orcefieldtools.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
> co
> rrespondence; 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.ff13q4mdfftData are 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.in file is:>> source > leaprc.gaffsource > leaprc.ff10leaprc.f> f03.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 >
> com
> p.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 >
> num
> bering 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?2> 8? 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) > d> oes _not_ perform atom typing (R.E.D. Python > does). You need to > define the atom
> ty
> pes 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 > D> MSO 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 > -0.8569> 33>> 0.225852 CT 1 DMSO > -0.2897 **** 2 H11 1.336243
> -1.8
> 43530 > -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 SXs
> et D> MSO.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#22rega
> rds,>> > > Francois> I am trying to prepare the input files for
> ambe> r>> > 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 com> p.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: ./frcmodReadi> ng > 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>Creat> ed > a new atom named: O1B
> within residue: > .R<G39>> 469>Created a > new atom > named: C2
> within resid
> ue: .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 at
> om 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 t> ype 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> <at> om2> > [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 fo
> r 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: 7> 7.502 > 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 > 1.5
> 00000 > for > O10) (u> sing>> 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>> 0> 000
> 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 b
> uild: 1 > secSolvent>> > present: replacing closest w> ith >
> 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 typ> > e.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 tha> t cause the
> errors, > Could you > help>> me figure it out? Thanks i
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Received on Sun Jul 07 2013 - 09:00:03 PDT
