*prepin file looks like:*
0 0 2
This is a remark line
DRG.res
DRG INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C c3 M 3 2 1 1.540 111.208 180.000 -0.101600
5 H hc E 4 3 2 1.091 104.545 142.425 0.046100
6 H1 hc E 4 3 2 1.088 146.672 -43.441 0.051400
7 H2 hc E 4 3 2 1.088 62.164 38.585 0.051500
8 C1 c3 M 4 3 2 1.530 54.427 -112.092 0.141200
9 H3 h1 E 8 4 3 1.091 108.397 -150.818 0.052800
10 H4 h1 E 8 4 3 1.091 111.541 -30.280 0.051100
11 O os M 8 4 3 1.448 108.137 91.084 -0.425900
12 C2 c M 11 8 4 1.349 118.617 168.687 0.648100
13 O1 o E 12 11 8 1.211 122.965 9.758 -0.554700
14 C3 ce M 12 11 8 1.476 115.008 -167.161 -0.090600
15 C29 cg S 14 12 11 1.437 115.929 -21.133 0.214900
16 N3 n1 E 15 14 12 1.141 173.617 -147.891 -0.366600
17 C4 cf M 14 12 11 1.348 123.438 163.594 0.059400
18 H5 ha E 17 14 12 1.089 115.511 11.355 0.156400
19 C5 ca M 17 14 12 1.488 126.441 -176.925 -0.172300
20 C6 ca B 19 17 14 1.394 120.232 -156.394 -0.046700
21 H6 ha E 20 19 17 1.088 120.806 -3.195 0.134000
22 C7 ca S 20 19 17 1.397 120.366 172.782 -0.217400
23 H7 ha E 22 20 19 1.086 118.344 -176.227 0.138000
24 C10 ca M 19 17 14 1.398 122.088 24.500 -0.038200
25 H9 ha E 24 19 17 1.083 122.005 8.338 0.144100
26 C9 ca M 24 19 17 1.382 121.699 -174.263 -0.220900
27 H8 ha E 26 24 19 1.083 116.412 177.889 0.140000
28 C8 ca M 26 24 19 1.393 120.446 -0.046 0.244200
29 N nh M 28 26 24 1.375 120.813 176.019 -0.699400
30 C11 c3 3 29 28 26 1.470 123.272 15.314 0.223100
*FRCMOD file is:*
remark goes here
MASS
BOND
ANGLE
os-c -ce 68.128 112.135 Calculated with empirical approach
c -ce-cg 64.498 117.800 Calculated with empirical approach
ce-cf-ca 65.200 123.080 same as c2-cf-ca
cg-ce-cf 66.500 122.220 same as c2-ce-cg
DIHE
c -ce-cg-n1 1 0.000 180.000 2.000 same as X
-c1-ce-X
ce-cf-ca-ca 1 2.550 180.000 2.000 same as X
-c2-ca-X
n1-cg-ce-cf 1 0.000 180.000 2.000 same as X
-c1-ce-X
ha-cf-ca-ca 1 2.550 180.000 2.000 same as X
-c2-ca-X
IMPROPER
ce-o -c -os 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
c -cf-ce-cg 1.1 180.0 2.0 Using default
value
ca-ce-cf-ha 1.1 180.0 2.0 Using default
value
ca-ca-ca-cf 1.1 180.0 2.0 Using default
value
ca-ca-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
ca-ca-ca-nh 1.1 180.0 2.0 Using default
value
c3-c3-nh-ca 1.1 180.0 2.0 Using default
value
c -c -n -c3 1.1 180.0 2.0 Using default
value
ca-n -c -o 10.5 180.0 2.0 General
improper torsional angle (2 general atom types)
c -ca-ca-ca 1.1 180.0 2.0 Using default
value
ca-ca-ca-ca 1.1 180.0 2.0 Using default
value
NONBON
On Fri, Nov 7, 2014 at 1:11 PM, Ruchika Bhat <ruchikabhat31.gmail.com>
wrote:
> Tried doing with mol2 file also but same error.
>
> > a= loadpdb pdb1_10854218DOCK.pdb
> Loading PDB file: ./pdb1_10854218DOCK.pdb
> Created a new atom named: OXT within residue: .R<CYS 212>
> ERROR: Comparing atoms
> .R<CYS 212>.A<C 10>,
> .R<DRG 1>.A<H 2>,
> .R<DRG 1>.A<H1 3>, and
> .R<DRG 1>.A<H2 4>
> to atoms
> .R<DRG 1>.A<C1 5>,
> .R<CYS 212>.A<C 10>,
> .R<DRG 1>.A<H2 4>, and
> .R<DRG 1>.A<H 2>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 140
> !FATAL: Message: Atom named C1 from DRG did not match !
> !
> !ABORTING.
>
>
>
> Thanks for helping.
>
>
> Best regards,
> Ruchika
>
> On Fri, Nov 7, 2014 at 9:52 AM, Wei Ye <yw20055968.126.com> wrote:
>
>> First, make sure the file to make prepin and frcmod are correct. I
>> recommend using MOL2 file format to do anetchamber.
>> Then, when you do tleap, delete all the CONECT information in the complex
>> pdb. This information has been stored in prepin file.
>> And make sure all the atom names are correct in the complex pdb with
>> prepin file.
>>
>>
>> HTH,
>> Wei.
>> 在2014年11月07 22时47分, "Ruchika Bhat"<ruchikabhat31.gmail.com>写道:
>>
>> *This is the error it is showing :*
>>
>> > source leaprc.gaff
>> ----- Source: /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd/leaprc.gaff
>> ----- Source of /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd/leaprc.gaff
>> done
>> Log file: ./leap.log
>> Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/gaff.dat
>> Reading title:
>> AMBER General Force Field for organic mol., add. info. at the end (June,
>> 2003)
>> > loadamberprep ligand1DRG.prepin
>> Loading Prep file: ./ligand1DRG.prepin
>> > loadamberparams ligand1drg.frcmod
>> Loading parameters: ./ligand1drg.frcmod
>> Reading force field modification type file (frcmod)
>> Reading title:
>> remark goes here
>> > a = loadpdb pdb1_10854218DOCK.pdb
>> Loading PDB file: ./pdb1_10854218DOCK.pdb
>> Created a new atom named: OXT within residue: .R<CYS 212>
>> ERROR: Comparing atoms
>> .R<CYS 212>.A<C 10>,
>> .R<DRG 1>.A<H 2>,
>> .R<DRG 1>.A<H1 3>, and
>> .R<DRG 1>.A<H2 4>
>> to atoms
>> .R<DRG 1>.A<C1 5>,
>> .R<CYS 212>.A<C 10>,
>> .R<DRG 1>.A<H2 4>, and
>> .R<DRG 1>.A<H 2>
>> This error may be due to faulty Connection atoms.
>> !FATAL ERROR----------------------------------------
>> !FATAL: In file [chirality.c], line 140
>> !FATAL: Message: Atom named C1 from DRG did not match !
>> !
>> !ABORTING.
>>
>> On Fri, Nov 7, 2014 at 8:08 PM, Gulsevin,Alican <agulsevin.ufl.edu>
>> wrote:
>>
>> > It can be several things. Your ligand has atoms AMBER does not
>> > recognize, check the frcmod file for sometimes antechamber is not able
>> > to recognize particular atoms and generates void parameters, which are
>> > not recognized later by tleap. Also, you need to load the frcmod file
>> > before you read the pdb, I don't know if that's the problem because you
>> > don't have your leap script here, but checking it can be useful as well.
>> >
>> > Alican
>> >
>> > On Fri, 7 Nov 2014 19:09:07 +0530, Ruchika Bhat wrote:
>> > > ?Hi everyone,
>> > >
>> > > Please guide me what is the command to generate the top and crd file
>> > > once I
>> > > generated the frcmod and prepin files.
>> > >
>> > > In the command
>> > >> saveamberparm DRG ligand.prmtop ligand.inpcrd
>> > >
>> > > The DRG = loadpdb pdb1_10854218DOCK.pdb
>> > >
>> > > But when I load the DRG with the protein ligand complex it is giving:
>> > >
>> > >
>> > > Loading PDB file: ./pdb1_10854218DOCK.pdb
>> > > Unknown residue: DRG number: 212 type: Terminal/last
>> > > ..relaxing end constraints to try for a dbase match
>> > > -no luck
>> > > Created a new atom named: OXT within residue: .R<CYS 212>
>> > > Creating new UNIT for residue: DRG sequence: 213
>> > > One sided connection. Residue: missing connect0 atom.
>> > > Created a new atom named: C within residue: .R<DRG 213>
>> > > Created a new atom named: H within residue: .R<DRG 213>
>> > > Created a new atom named: H1 within residue: .R<DRG 213>
>> > > Created a new atom named: H2 within residue: .R<DRG 213>
>> > > Created a new atom named: C1 within residue: .R<DRG 213>
>> > > Created a new atom named: H3 within residue: .R<DRG 213>
>> > > Created a new atom named: H4 within residue: .R<DRG 213>
>> > > Created a new atom named: O within residue: .R<DRG 213>
>> > > Created a new atom named: C2 within residue: .R<DRG 213>
>> > > Created a new atom named: O1 within residue: .R<DRG 213>
>> > > Created a new atom named: C3 within residue: .R<DRG 213>
>> > > Created a new atom named: C29 within residue: .R<DRG 213>
>> > > Created a new atom named: N3 within residue: .R<DRG 213>
>> > > Created a new atom named: C4 within residue: .R<DRG 213>
>> > > Created a new atom named: H5 within residue: .R<DRG 213>
>> > > Created a new atom named: C5 within residue: .R<DRG 213>
>> > > Created a new atom named: C10 within residue: .R<DRG 213>
>> > > Created a new atom named: C9 within residue: .R<DRG 213>
>> > > Created a new atom named: H8 within residue: .R<DRG 213>
>> > > Created a new atom named: H9 within residue: .R<DRG 213>
>> > > Created a new atom named: C6 within residue: .R<DRG 213>
>> > > Created a new atom named: H6 within residue: .R<DRG 213>
>> > > Created a new atom named: C7 within residue: .R<DRG 213>
>> > > Created a new atom named: H7 within residue: .R<DRG 213>
>> > > Created a new atom named: C8 within residue: .R<DRG 213>
>> > > Created a new atom named: N within residue: .R<DRG 213>
>> > > Created a new atom named: C14 within residue: .R<DRG 213>
>> > > Created a new atom named: C13 within residue: .R<DRG 213>
>> > > Created a new atom named: H14 within residue: .R<DRG 213>
>> > > Created a new atom named: H15 within residue: .R<DRG 213>
>> > > Created a new atom named: H16 within residue: .R<DRG 213>
>> > > Created a new atom named: H17 within residue: .R<DRG 213>
>> > > Created a new atom named: C11 within residue: .R<DRG 213>
>> > > Created a new atom named: H10 within residue: .R<DRG 213>
>> > > Created a new atom named: H11 within residue: .R<DRG 213>
>> > > Created a new atom named: C12 within residue: .R<DRG 213>
>> > > Created a new atom named: H12 within residue: .R<DRG 213>
>> > > Created a new atom named: H13 within residue: .R<DRG 213>
>> > > Created a new atom named: N1 within residue: .R<DRG 213>
>> > > Created a new atom named: C15 within residue: .R<DRG 213>
>> > > Created a new atom named: H18 within residue: .R<DRG 213>
>> > > Created a new atom named: H19 within residue: .R<DRG 213>
>> > > Created a new atom named: C16 within residue: .R<DRG 213>
>> > > Created a new atom named: H20 within residue: .R<DRG 213>
>> > > Created a new atom named: H21 within residue: .R<DRG 213>
>> > > Created a new atom named: N2 within residue: .R<DRG 213>
>> > > Created a new atom named: C28 within residue: .R<DRG 213>
>> > > Created a new atom named: O3 within residue: .R<DRG 213>
>> > > Created a new atom named: C17 within residue: .R<DRG 213>
>> > > Created a new atom named: O2 within residue: .R<DRG 213>
>> > > Created a new atom named: C18 within residue: .R<DRG 213>
>> > > Created a new atom named: C19 within residue: .R<DRG 213>
>> > > Created a new atom named: H22 within residue: .R<DRG 213>
>> > > Created a new atom named: C20 within residue: .R<DRG 213>
>> > > Created a new atom named: H23 within residue: .R<DRG 213>
>> > > Created a new atom named: C21 within residue: .R<DRG 213>
>> > > Created a new atom named: H24 within residue: .R<DRG 213>
>> > > Created a new atom named: C22 within residue: .R<DRG 213>
>> > > Created a new atom named: C23 within residue: .R<DRG 213>
>> > > Created a new atom named: C24 within residue: .R<DRG 213>
>> > > Created a new atom named: C25 within residue: .R<DRG 213>
>> > > Created a new atom named: H25 within residue: .R<DRG 213>
>> > > Created a new atom named: C26 within residue: .R<DRG 213>
>> > > Created a new atom named: H26 within residue: .R<DRG 213>
>> > > Created a new atom named: C27 within residue: .R<DRG 213>
>> > > Created a new atom named: H27 within residue: .R<DRG 213>
>> > > total atoms in file: 3493
>> > > The file contained 67 atoms not in residue templates
>> > >
>> > >
>> > > *Please help me with how to proceed with making top and crd files,
>> > > after I
>> > > generated the prepin and frcmod files.*
>> > >
>> > > Thanking for your valuable time and guidance.
>> > >
>> > > Best Regards,
>> > > Ruchika
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>
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Received on Fri Nov 07 2014 - 10:30:03 PST
