Hi all again,
The overall situation is a little bit strange since I never encountered any
problem before and I am encountering problem right now with this system..
And If I tried to re-do another ligand that start with a digit is not
working any more while before was working!
So I resolved by changing its name and it is now working..
For more information check below
*cat kira.pdb*
HEADER TRANSFERASE/TRANSFERASE INHIBITOR
REMARK 99
REMARK 99 MOE v2018.01 (Chemical Computing Group ULC) Wed Oct 03 07:58:53
2018
HETATM 1 C21 *SE1* 1 -5.809 -25.013 -1.347 1.00
28.83 C
HETATM 2 C22 SE1 1 -6.027 -26.352 -1.984 1.00
28.29 C
HETATM 3 C23 SE1 1 -5.825 -26.262 -3.449 1.00
29.90 C
HETATM 4 N6 SE1 1 -5.846 -27.585 -3.996 1.00
30.56 N1+
HETATM 5 C24 SE1 1 -4.499 -25.634 -3.790 1.00 29.33
C
HETATM 6 C25 SE1 1 -4.231 -24.356 -3.050 1.00
29.07 C
HETATM 7 C20 SE1 1 -4.417 -24.526 -1.568 1.00
28.65 C
HETATM 8 N4 SE1 1 -4.235 -23.289 -0.849 1.00
29.41 N
HETATM 9 C12 SE1 1 -3.075 -22.799 -0.595 1.00
28.33 C
HETATM 10 N2 SE1 1 -2.049 -23.578 -0.564 1.00
27.26 N
HETATM 11 N3 SE1 1 -2.951 -21.519 -0.367 1.00
28.51 N
HETATM 12 C15 SE1 1 -1.802 -20.987 -0.118 1.00
27.41 C
HETATM 13 C13 SE1 1 -0.707 -21.795 -0.075 1.00
28.17 C
HETATM 14 C11 SE1 1 -0.861 -23.129 -0.321 1.00
28.55 C
HETATM 15 C14 SE1 1 0.159 -24.050 -0.268 1.00
29.20 C
HETATM 16 C16 SE1 1 -0.225 -25.351 -0.151 1.00
29.51 C
HETATM 17 C17 SE1 1 0.709 -26.329 -0.071 1.00
30.25 C
HETATM 18 C18 SE1 1 2.004 -25.949 -0.090 1.00
29.15 C
HETATM 19 N5 SE1 1 2.353 -24.704 -0.180 1.00
31.20 N
HETATM 20 C19 SE1 1 1.490 -23.733 -0.262 1.00
30.43 C
HETATM 21 O1 SE1 1 1.878 -22.456 -0.368 1.00
33.20 O
HETATM 22 C4 SE1 1 3.082 -22.014 -0.053 1.00
32.88 C
HETATM 23 C5 SE1 1 4.067 -21.896 -0.986 1.00
33.33 C
HETATM 24 C26 SE1 1 3.877 -22.331 -2.400 1.00
31.42 C
HETATM 25 C6 SE1 1 5.291 -21.432 -0.635 1.00
35.10 C
HETATM 26 C3 SE1 1 3.320 -21.591 1.202 1.00
32.48 C
HETATM 27 C10 SE1 1 2.331 -21.678 2.130 1.00
32.06 C
HETATM 28 C9 SE1 1 2.539 -21.287 3.422 1.00
30.89 C
HETATM 29 C8 SE1 1 3.752 -20.783 3.782 1.00
31.14 C
HETATM 30 C7 SE1 1 4.752 -20.693 2.849 1.00
32.17 C
HETATM 31 C2 SE1 1 4.538 -21.102 1.562 1.00
33.82 C
HETATM 32 C1 SE1 1 5.537 -21.021 0.633 1.00
36.52 C
HETATM 33 N1 SE1 1 6.707 -20.546 0.921 1.00
41.72 N
HETATM 34 S1 SE1 1 7.174 -19.117 0.354 1.00
51.09 S2+
HETATM 35 O2 SE1 1 6.399 -18.653 -0.786 1.00
47.06 O1-
HETATM 36 O3 SE1 1 8.558 -19.217 0.080 1.00
51.10 O1-
HETATM 37 C27 SE1 1 6.924 -17.844 1.373 1.00
52.56 C
HETATM 38 C32 SE1 1 5.965 -16.970 0.938 1.00
52.06 C
HETATM 39 C31 SE1 1 5.680 -15.873 1.712 1.00
52.33 C
HETATM 40 C30 SE1 1 6.331 -15.660 2.902 1.00
52.15 C
HETATM 41 C29 SE1 1 7.283 -16.528 3.332 1.00
52.63 C
HETATM 42 C28 SE1 1 7.572 -17.606 2.566 1.00
53.23 C
HETATM 43 CL1 SE1 1 8.756 -18.621 3.183 1.00 63.38
CL
HETATM 44 H211 SE1 1 -6.003 -25.106 -0.276 1.00
0.00 H
HETATM 45 H212 SE1 1 -6.547 -24.299 -1.723 1.00
0.00 H
HETATM 46 H221 SE1 1 -7.038 -26.701 -1.763 1.00
0.00 H
HETATM 47 H222 SE1 1 -5.350 -27.082 -1.531 1.00
0.00 H
HETATM 48 H23 SE1 1 -6.644 -25.730 -3.935 1.00
0.00 H
HETATM 49 H61 SE1 1 -5.625 -27.571 -4.992 1.00
0.00 H
HETATM 50 H62 SE1 1 -5.157 -28.164 -3.539 1.00
0.00 H
HETATM 51 H63 SE1 1 -6.757 -28.004 -3.878 1.00
0.00 H
HETATM 52 H241 SE1 1 -4.438 -25.453 -4.864 1.00
0.00 H
HETATM 53 H242 SE1 1 -3.683 -26.327 -3.568 1.00
0.00 H
HETATM 54 H251 SE1 1 -4.892 -23.573 -3.430 1.00
0.00 H
HETATM 55 H252 SE1 1 -3.216 -24.021 -3.270 1.00
0.00 H
HETATM 56 H20 SE1 1 -3.717 -25.275 -1.190 1.00
0.00 H
HETATM 57 HN4 SE1 1 -4.988 -22.619 -0.927 1.00
0.00 H
HETATM 58 H15 SE1 1 -1.755 -19.925 0.078 1.00
0.00 H
HETATM 59 H13 SE1 1 0.190 -21.282 0.210 1.00
0.00 H
HETATM 60 H16 SE1 1 -1.245 -25.705 -0.109 1.00
0.00 H
HETATM 61 H17 SE1 1 0.428 -27.368 0.017 1.00
0.00 H
HETATM 62 H18 SE1 1 2.800 -26.677 -0.025 1.00
0.00 H
HETATM 63 H261 SE1 1 4.757 -22.175 -3.020 1.00
0.00 H
HETATM 64 H262 SE1 1 3.639 -23.394 -2.440 1.00
0.00 H
HETATM 65 H263 SE1 1 3.050 -21.784 -2.854 1.00
0.00 H
HETATM 66 H6 SE1 1 6.080 -21.413 -1.367 1.00
0.00 H
HETATM 67 H10 SE1 1 1.358 -22.078 1.893 1.00
0.00 H
HETATM 68 H9 SE1 1 1.748 -21.369 4.153 1.00
0.00 H
HETATM 69 H8 SE1 1 3.916 -20.451 4.796 1.00
0.00 H
HETATM 70 H7 SE1 1 5.701 -20.287 3.168 1.00
0.00 H
HETATM 71 HN1 SE1 1 6.936 -20.616 1.900 1.00
0.00 H
HETATM 72 H32 SE1 1 5.327 -17.021 0.069 1.00
0.00 H
HETATM 73 H31 SE1 1 4.892 -15.210 1.392 1.00
0.00 H
HETATM 74 H30 SE1 1 6.093 -14.789 3.493 1.00
0.00 H
HETATM 75 H29 SE1 1 7.796 -16.349 4.266 1.00
0.00 H
END
> *source leaprc.gaff*
----- Source: /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /Users/Antonio/Desktop/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /Users/Antonio/Desktop/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
*> SE1 = loadmol2 kira.mol2*
Loading Mol2 file: ./kira.mol2
Reading MOLECULE named SE1
> *list*
A A3 A5 ACE AG AL ALA AN
ARG ASH ASN ASP Ag BA BR Be
C C3 C5 CA CALA CARG CASN CASP
CCYS CCYX CD CE CGLN CGLU CGLY
CHCL3BOX
CHID CHIE CHIP CHIS CHYP CILE CL CLEU
CLYS CMET CN CO CPHE CPRO CR CS
CSER CTHR CTRP CTYR CU CU1 CVAL CYM
CYS CYX Ce Cl- Cr DA DA3 DA5
DAN DC DC3 DC4 DC5 DCN DG DG3
DG5 DGN DT DT3 DT5 DTN Dy EU
EU3 Er F FB3 FB3BOX FB4 FB4BOX FE
FE2 G G3 G5 GD3 GLH GLN GLU
GLY GN H3O+ HE+ HG HID HIE HIP
HIS HOH HYP HZ+ Hf ILE IN IOD
K K+ LA LEU LI LU LYN LYS
MEOHBOX MET MG MN NA NALA NARG NASN
NASP NCYS NCYX NGLN NGLU NGLY NH4 NHE
NHID NHIE NHIP NHIS NI NILE NLEU NLYS
NMABOX NME NMET NPHE NPRO NSER NTHR NTRP
NTYR NVAL Na+ Nd OHE OP3 OPC
OPC3BOX
OPCBOX PB PD PHE PL3 POL3BOX PR PRO
PT Pu QSPCFWBOX RB Ra S2P *SE1*
SER
SM SPC SPCBOX SPCFWBOX SPF SPG SR Sm
Sn T2P T4E TB THR TIP3PBOX TIP3PFBOX
TIP4PBOX
TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF TRP
TYR Th Tl Tm U U3 U4+ U5
UN V2+ VAL WAT Y YB2 ZN Zr
On Wed, Oct 3, 2018 at 1:50 PM David Case <david.case.rutgers.edu> wrote:
> On Wed, Oct 03, 2018, Antonio Amber Carlesso wrote:
>
> > > *3E4 = loadmol2 kira.mol2*
> > Error: Error from the parser: syntax error
>
> Aargh! I spoke too soon in my previous post. The parsing problem only
> comes
> when the unit name is entirely digits (like "313"). I'm unable to
> reproduce
> the behavior you report above:
>
> > 3R0 = loadmol2 3R0.mol2
> Loading Mol2 file: ./3R0.mol2
> Reading MOLECULE named 3R0
> > list
> 3R0
>
> I'm not even sure what questions to ask to narrow down the problem. I
> guess
> it might help to know which version of AmberTools you are using, and what
> OS and compiler. Can you try running this example on a different computer?
> Can you think of anything that is odd about your installation?
>
> [Aside: it would still be nice if the syntax for loadMol2 matched that for
> loadOff, but only if that turns out to be easy to do....]
>
> ....dac
>
>
> _______________________________________________
> 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
Received on Wed Oct 03 2018 - 07:30:03 PDT
