Jason,
Thank you for your help! Yes, the pdb makes sense above the HETATMs, I
jsut didnt include the complete pdb so that my email was shorter. I
also am not going to use this in any simulation. I calculated charges
with gaussian and antechamber and I want to create a pdb now with ambpdb
and to do that I need a top and crd file (this is how I was taught maybe
different way). So i am not going got simulate anything, I just want to
have a pdb that has amber radii and charges from the resp calculation.
If you know of a good tutorial on how to calculate your own parameters
for the items that need attention in my files I would love if you could
point me to them.
Thank you again for all your help and fast reply.
Don
On 11/03/2009 09:29 PM, Jason Swails wrote:
> Hello,
>
> The error messages tell you exactly what's happening. The PDB doesn't make
> much sense before the TER card (all I see are hydrogens), so I'll just
> assume that whatever comes before that causes the PDB to make sense. The
> problem is that you are confusing atom NAMES with atom TYPES in your PDB.
> In the PDB, each atom should be given its NAME, not its TYPE. Instead of
> having the atoms be labeled NT, CT, CT, SO, O, O, C, O, H1, H1, HS, H, H,
> H1, HA, have them labeled by the name given to them in the library file.
> (First column are names, second are types). This would be N, C, C1, S, O,
> O1, C2, O2, H, H1, H2, H3, H4, H5, H6. It was complaining because several
> of these atoms are given the same NAME in the pdb (H and H1 have the same
> TYPE, but different NAMES). Replacing the atom TYPES with atom NAMES in the
> pdb should be able to make your prmtop file.
>
> However, the frcmod file is warning you in several instances. Parmchk,
> which I believe you used to create your frcmod file, looks through a
> parameter database for relevant parameters to add. If there's a parameter
> that exists in your molecule (for example, an S-O bond between types O and
> SO), and it can't find a sensible substitute in the parameter database, it
> inserts a line and zeroes all of the parameters, saying "ATTN, needs
> revision". Thus, if you use any prmtop created by that frcmod, you will
> certainly get wrong results. Thus, for each line in the frcmod file that
> says "ATTN, needs revision", you need to find (or calculate) the appropriate
> parameter. There are several other threads in which people have posted
> locations of custom parameters, so you can search the mailing list for these
> instances. As it stands right now, though, your frcmod should not be used
> to create a topology file that you use in simulations.
>
> Good luck!
> Jason
>
> On Tue, Nov 3, 2009 at 11:47 PM, Donald Keidel<dkeidel.scripps.edu> wrote:
>
>
>> Hi,
>>
>> I have created the following files:
>>
>> 1. SOC_amber.frcmod
>> 2. SOC_amber.lib
>> 3. SOC_Min1_amber.prepi
>>
>>
>> Using tutorials I have used before that I was successful with on other
>> small molecules.
>>
>> I could not attach them even if I zipped them so I have pasted them at the
>> bottom of this email. The complete pdb is not attched, only the relevant
>> coordinates.
>>
>> I load the the .lib and frcmod into tleap along with a pdb that has what I
>> think are correct corresponding types.
>>
>> I execute the following commands in tleap:
>>
>> tleap
>>
>>
>>> loadoff SOC_amber.lib
>>>
>> Loading library: ./SOC_amber.lib
>>
>>> loadamberparams SOC_amber.frcmod
>>>
>> Loading parameters: ./SOC_amber.frcmod
>> Reading force field modification type file (frcmod) Reading title:
>> remark goes here
>>
>>> prot= loadPdb 2SNI_r_u_TERENDFH_cyx_his.pdb
>>>
>> Loading PDB file: ./2SNI_r_u_TERENDFH_cyx_his.pdb
>> -- residue 275: duplicate [ CT] atoms (total 2)
>> -- residue 275: duplicate [ H] atoms (total 2)
>> -- residue 275: duplicate [ H1] atoms (total 3)
>> -- residue 275: duplicate [ O] atoms (total 3)
>>
>> Warning: Atom names in each residue should be unique.
>> (Same-name atoms are handled by using the first
>> occurrence and by ignoring the rest.
>> Frequently duplicate atom names stem from alternate
>> conformations in the PDB file.)
>>
>> Added missing heavy atom: .R<CGLN 274>.A<OXT 18>
>> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported ---Tried to
>> +superimpose torsions for: *-C1-S-*
>> +--- With Sp3 - Sp0
>> +--- Sp0 probably means a new atom type is involved
>> +--- which needs to be added via addAtomTypes
>> Created a new atom named: NT within residue: .R<SOC 275> Created a new atom
>> named: CT within residue: .R<SOC 275> Created a new atom named: SO within
>> residue: .R<SOC 275> Created a new atom named: HS within residue: .R<SOC
>> 275> Created a new atom named: HA within residue: .R<SOC 275>
>> Added missing heavy atom: .R<SOC 275>.A<N 1>
>> Added missing heavy atom: .R<SOC 275>.A<C1 3>
>> Added missing heavy atom: .R<SOC 275>.A<C2 7>
>> Added missing heavy atom: .R<SOC 275>.A<S 4>
>> Added missing heavy atom: .R<SOC 275>.A<O2 8>
>> Added missing heavy atom: .R<SOC 275>.A<O1 6>
>> total atoms in file: 3840
>> Leap added 13 missing atoms according to residue templates:
>> 7 Heavy
>> 6 H / lone pairs
>> The file contained 5 atoms not in residue templates
>>
>>> saveAmberParm prot 2SNI_r_u_ToMin.top 2SNI_r_u_ToMin.crd
>>>
>> Checking Unit.
>> WARNING: There is a bond of 3.141250 angstroms between:
>> ------- .R<THR 220>.A<C 13> and .R<MET 221>.A<N 1>
>> WARNING: There is a bond of 4.802990 angstroms between:
>> ------- .R<SOC 275>.A<C1 3> and .R<SOC 275>.A<H 9>
>> WARNING: There is a bond of 3.352835 angstroms between:
>> ------- .R<SOC 275>.A<C1 3> and .R<SOC 275>.A<H1 10>
>> WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
>> WARNING: The perturbed charge: -1.000001 is not zero.
>> FATAL: Atom .R<SOC 275>.A<NT 16> does not have a type.
>> FATAL: Atom .R<SOC 275>.A<CT 17> does not have a type.
>> FATAL: Atom .R<SOC 275>.A<SO 18> does not have a type.
>> FATAL: Atom .R<SOC 275>.A<HS 19> does not have a type.
>> FATAL: Atom .R<SOC 275>.A<HA 20> does not have a type.
>> Failed to generate parameters
>> Parameter file was not saved.
>>
>>
>>
>>
>> I get these FATAL warnings that I am not too sure why they appear in the
>> first place. I have looked at the .inp and frcmod files and as far as I can
>> see these atom types have been defined with forcefeild parameters.
>>
>> I am turning to the amber mailing list since it is not clear to me how this
>> can occur.
>>
>> I appreciate all help and look forward to any responses.
>>
>> Thank you
>>
>> Don Keidel
>>
>>
>>
>>
>> .lib file:
>>
>> !!index array str
>> "SOC"
>> !entry.SOC.unit.atoms table str name str type int typex int resx int
>> flags int seq int elmnt dbl chg
>> "N" "NT" 0 1 131075 1 7 0.0
>> "C" "CT" 0 1 131075 2 6 0.0
>> "C1" "CT" 0 1 131075 3 6 0.0
>> "S" "SO" 0 1 131075 4 16 0.0
>> "O" "O" 0 1 131075 5 8 0.0
>> "O1" "O" 0 1 131075 6 8 0.0
>> "C2" "C" 0 1 131075 7 6 0.0
>> "O2" "O" 0 1 131075 8 8 0.0
>> "H" "H1" 0 1 131075 9 1 0.0
>> "H1" "H1" 0 1 131075 10 1 0.0
>> "H2" "HS" 0 1 131075 11 1 0.0
>> "H3" "H" 0 1 131075 12 1 0.0
>> "H4" "H" 0 1 131075 13 1 0.0
>> "H5" "H1" 0 1 131075 14 1 0.0
>> "H6" "HA" 0 1 131075 15 1 0.0
>> !entry.SOC.unit.atomspertinfo table str pname str ptype int ptypex int
>> pelmnt dbl pchg
>> "N" "NT" 0 -1 -0.979650
>> "C" "CT" 0 -1 0.391374
>> "C1" "CT" 0 -1 -0.507566
>> "S" "SO" 0 -1 0.863455
>> "O" "O" 0 -1 -0.479112
>> "O1" "O" 0 -1 -0.479112
>> "C2" "C" 0 -1 0.392243
>> "O2" "O" 0 -1 -0.424901
>> "H" "H1" 0 -1 0.184693
>> "H1" "H1" 0 -1 0.184693
>> "H2" "HS" 0 -1 0.054947
>> "H3" "H" 0 -1 0.378500
>> "H4" "H" 0 -1 0.378500
>> "H5" "H1" 0 -1 0.030276
>> "H6" "HA" 0 -1 0.011659
>> !entry.SOC.unit.boundbox array dbl
>> -1.000000
>> 0.0
>> 0.0
>> 0.0
>> 0.0
>> !entry.SOC.unit.childsequence single int
>> 2
>> !entry.SOC.unit.connect array int
>> 0
>> 0
>> !entry.SOC.unit.connectivity table int atom1x int atom2x int flags
>> 1 2 1
>> 1 13 1
>> 1 12 1
>> 2 3 1
>> 2 7 1
>> 2 14 1
>> 3 4 1
>> 3 9 1
>> 3 10 1
>> 4 5 1
>> 4 11 1
>> 4 6 1
>> 7 15 1
>> 7 8 1
>> !entry.SOC.unit.hierarchy table str abovetype int abovex str belowtype
>> int belowx
>> "U" 0 "R" 1
>> "R" 1 "A" 1
>> "R" 1 "A" 2
>> "R" 1 "A" 3
>> "R" 1 "A" 4
>> "R" 1 "A" 5
>> "R" 1 "A" 6
>> "R" 1 "A" 7
>> "R" 1 "A" 8
>> "R" 1 "A" 9
>> "R" 1 "A" 10
>> "R" 1 "A" 11
>> "R" 1 "A" 12
>> "R" 1 "A" 13
>> "R" 1 "A" 14
>> "R" 1 "A" 15
>> !entry.SOC.unit.name single str
>> ""
>> !entry.SOC.unit.positions table dbl x dbl y dbl z
>> 12.620000 -4.114000 9.406000
>> 12.866000 -2.722000 9.686000
>> 13.066000 -1.904000 8.373000
>> 13.638000 -2.652000 6.775000
>> 12.436000 -2.021000 5.718000
>> 13.301000 -4.323000 6.612000
>> 11.690000 -2.134000 10.454000
>> 11.892000 -1.134000 11.135000
>> 12.045000 -1.551000 8.226000
>> 13.839000 -1.213000 8.710000
>> 14.925000 -2.474000 6.544000
>> 11.672000 -4.450000 9.308000
>> 13.395000 -4.754000 9.308000
>> 13.769000 -2.732000 10.296000
>> 10.648000 -2.446000 10.520000
>> !entry.SOC.unit.residueconnect table int c1x int c2x int c3x int c4x
>> int c5x int c6x
>> 0 0 0 0 0 0
>> !entry.SOC.unit.residues table str name int seq int childseq int
>> startatomx str restype int imagingx
>> "SOC" 1 16 1 "?" 0
>> !entry.SOC.unit.residuesPdbSequenceNumber array int
>> 1
>> !entry.SOC.unit.solventcap array dbl
>> -1.000000
>> 0.0
>> 0.0
>> 0.0
>> 0.0
>> !entry.SOC.unit.velocities table dbl x dbl y dbl z
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>> 0.0 0.0 0.0
>>
>>
>> Frcmod file:
>>
>> remark goes here
>> MASS
>> O 16.000 0.434 same as o
>> SO 0.000 0.000 ATTN, need revision
>> HS 1.008 0.135 same as hs
>> CT 12.010 0.878 same as c3
>> H1 1.008 0.135 same as hc
>> NT 14.010 0.530 same as n3
>> H 1.008 0.161 same as hn
>> C 12.010 0.616 same as c
>> HA 1.008 0.135 same as hc
>>
>> BOND
>> O -SO 0.00 0.000 ATTN, need revision
>> SO-HS 0.00 0.000 ATTN, need revision
>> SO-CT 0.00 0.000 ATTN, need revision
>> CT-H1 337.30 1.092 same as c3-hc
>> CT-CT 303.10 1.535 same as c3-c3
>> CT-NT 320.60 1.470 same as c3-n3
>> CT-C 328.30 1.508 same as c -c3
>> NT-H 394.10 1.018 same as hn-n3
>> C -HA 0.00 0.000 ATTN, need revision
>> C -O 648.00 1.214 same as c -o
>>
>> ANGLE
>> O -SO-O 0.000 0.000 ATTN, need revision
>> O -SO-HS 0.000 0.000 ATTN, need revision
>> O -SO-CT 0.000 0.000 ATTN, need revision
>> SO-CT-H1 0.000 0.000 ATTN, need revision
>> SO-CT-CT 0.000 0.000 ATTN, need revision
>> HS-SO-CT 0.000 0.000 ATTN, need revision
>> CT-CT-NT 66.200 110.380 same as c3-c3-n3
>> CT-CT-H1 46.400 110.050 same as c3-c3-hc
>> CT-CT-C 63.800 110.530 same as c -c3-c3
>> H1-CT-H1 39.400 108.350 same as hc-c3-hc
>> CT-NT-H 47.100 109.920 same as c3-n3-hn
>> CT-C -HA 0.000 0.000 ATTN, need revision
>> CT-C -O 68.000 123.110 same as c3-c -o
>> NT-CT-H1 49.400 109.800 same as hc-c3-n3
>> NT-CT-C 65.800 113.910 same as c -c3-n3
>> H -NT-H 41.300 107.130 same as hn-n3-hn
>> H1-CT-C 47.200 109.680 same as c -c3-hc
>> HA-C -O 55.400 120.000 same as hc-c -o
>>
>> DIHE
>> O -SO-CT-H1 1 0.000 0.000 0.000 ATTN, need
>> revision
>> O -SO-CT-CT 1 0.000 0.000 0.000 ATTN, need
>> revision
>> SO-CT-CT-NT 1 0.000 0.000 0.000 ATTN, need
>> revision
>> SO-CT-CT-H1 1 0.000 0.000 0.000 ATTN, need
>> revision
>> SO-CT-CT-C 1 0.000 0.000 0.000 ATTN, need
>> revision
>> HS-SO-CT-H1 1 0.000 0.000 0.000 ATTN, need
>> revision
>> HS-SO-CT-CT 1 0.000 0.000 0.000 ATTN, need
>> revision
>> CT-CT-NT-H 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> CT-CT-C -HA 1 0.000 180.000 2.000 same as X -c
>> -c3-X
>> CT-CT-C -O 1 0.000 180.000 2.000 same as X -c
>> -c3-X
>> H1-CT-CT-NT 1 0.156 0.000 3.000 same as X
>> -c3-c3-X
>> H1-CT-CT-H1 1 0.150 0.000 3.000 same as
>> hc-c3-c3-hc
>> H1-CT-CT-C 1 0.156 0.000 3.000 same as X
>> -c3-c3-X
>> NT-CT-C -HA 1 0.000 180.000 2.000 same as X -c
>> -c3-X
>> NT-CT-C -O 1 0.000 180.000 2.000 same as X -c
>> -c3-X
>> H -NT-CT-H1 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> H -NT-CT-C 1 0.300 0.000 3.000 same as X
>> -c3-n3-X
>> H1-CT-C -HA 1 0.000 180.000 2.000 same as X -c
>> -c3-X
>> H1-CT-C -O 1 0.800 0.000 -1.000 same as hc-c3-c
>> -o
>> H1-CT-C -O 1 0.080 180.000 3.000 same as hc-c3-c
>> -o
>>
>> IMPROPER
>> CT-HA-C -O 1.1 180.0 2.0 Using default
>> value
>>
>> NONBON
>> O 1.6612 0.2100 same as o
>> SO 0.0000 0.0000 ATTN, need revision
>> HS 0.6000 0.0157 same as hs
>> CT 1.9080 0.1094 same as c3
>> H1 1.4870 0.0157 same as hc
>> NT 1.8240 0.1700 same as n3
>> H 0.6000 0.0157 same as hn
>> C 1.9080 0.0860 same as c
>> HA 1.4870 0.0157 same as hc
>>
>>
>> Coordinates from the pdb file used:
>>
>> .
>> .
>> .
>> ATOM 0 H GLN A 275 10.399 -6.157 33.952 1.00 20.40
>> H new
>> ATOM 0 HA GLN A 275 10.331 -6.646 36.146 1.00 24.09
>> H new
>> ATOM 0 HB2 GLN A 275 13.068 -5.364 35.790 1.00 26.61
>> H new
>> ATOM 0 HB3 GLN A 275 12.554 -6.041 37.341 1.00 26.61
>> H new
>> ATOM 0 HG2 GLN A 275 12.294 -8.274 36.236 1.00 35.29
>> H new
>> ATOM 0 HG3 GLN A 275 12.916 -7.573 34.737 1.00 35.29
>> H new
>> ATOM 0 HE21 GLN A 275 16.176 -8.271 35.674 1.00 43.93
>> H new
>> ATOM 0 HE22 GLN A 275 14.890 -8.408 34.521 1.00 43.93
>> H new
>> TER
>> HETATM 1 NT SOC 1 12.620 -4.114 9.406 1.00 0.00
>> HETATM 2 CT SOC 1 12.866 -2.722 9.686 1.00 0.00
>> HETATM 3 CT SOC 1 13.066 -1.904 8.373 1.00 0.00
>> HETATM 4 SO SOC 1 13.638 -2.652 6.775 1.00 0.00
>> HETATM 5 O SOC 1 12.436 -2.021 5.718 1.00 0.00
>> HETATM 6 O SOC 1 13.301 -4.323 6.612 1.00 0.00
>> HETATM 7 C SOC 1 11.690 -2.134 10.454 1.00 0.00
>> HETATM 8 O SOC 1 11.892 -1.134 11.135 1.00 0.00
>> HETATM 9 H1 SOC 1 12.045 -1.551 8.226 1.00 0.00
>> HETATM 10 H1 SOC 1 13.839 -1.213 8.710 1.00 0.00
>> HETATM 11 HS SOC 1 14.925 -2.474 6.544 1.00 0.00
>> HETATM 12 H SOC 1 11.672 -4.450 9.308 1.00 0.00
>> HETATM 13 H SOC 1 13.395 -4.754 9.308 1.00 0.00
>> HETATM 14 H1 SOC 1 13.769 -2.732 10.296 1.00 0.00
>> HETATM 15 HA SOC 1 10.648 -2.446 10.520 1.00 0.00
>> TER
>> END
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
"The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or repair."
-- One of the laws of computers and programming revealed
Douglas Adams in "Mostly Harmless"
_______________________________________________________________________
Donald J. Keidel, Ph.D.
Research Associate
The Scripps Research Institute
3377 N. Torrey Pines Court, Suite 100
La Jolla, CA 92037
mail code: TPC-26
phone: (858) 784-2842
fax: (858) 784-2341
dkeidel.scripps.edu
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm
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Received on Wed Nov 04 2009 - 10:00:04 PST
