Re: [AMBER] Help

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 14 Nov 2017 12:33:36 -0500

Hi,

Antechamber is not the correct program to use here; that is for
parameterizing small molecules. You want to use tleap to generate
topology/coordinate files from your PDB file. You may want to run the
PDB through pdb4amber first. Since you are new to this I recommend
doing a few of the beginner tutorials (http://ambermd.org/tutorials/)
as well as reading the tleap portion of the Amber manual first. Hope
this helps,

-Dan

On Tue, Nov 14, 2017 at 10:16 AM, Yuliia Varenyk <yvarenyk.genesilico.pl> wrote:
> Hello,
>
> I am using AmberTools17 on linux Mint 18, I am trying to run MD
> simulations on the pdb file 3ibk, and i can't since I have a problem
> with creation of topology and parameters files. Always some kind of
> errors connected to "weird bonds" occur. The last one looks like this:
>
> antechamber -i 3ibk.pdb -fi pdb -o 3ibk.mol2 -fo mol2 -c bcc -s 2
>
> Welcome to antechamber 17.3: molecular input file processor.
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for pdb File --
> Status: pass
> Warning: Detected more than 10 Residue sequence numbers;
> this may be a large multiple residue PDB file;
> large multiple residue PDB files are not supported.
> Continuing, but problems may be encountered.
> -- Check Unusual Elements --
> Warning: Unusual element (K) for atom (ID: 521, Name: K).
> Warning: Unusual element (K) for atom (ID: 522, Name: K).
> GAFF does not have sufficient parameters for molecules having unusual
> elements (those other than H,C,N,O,S,P and halogens).
> To ensure antechamber works properly, one may need to designate
> bond types for bonds involved with unusual elements.
> To do so, simply freeze the bond types by appending "F" or "f"
> to the corresponding bond types in ac or mol2 files.
> -- Check Open Valences --
> Status: pass
> -- Check Geometry --
> for those bonded
> Warning: Large distance for BOND 21 O6 K 0 2.84 [1.42 - 2.31]
> Warning: Large distance for BOND 22 O6 K 0 2.83 [1.42 - 2.31]
> Warning: Large distance for BOND 23 O6 K 0 2.96 [1.42 - 2.31]
> Warning: Large distance for BOND 24 O6 K 0 2.66 [1.42 - 2.31]
> Warning: Large distance for BOND 25 O6 K 0 2.74 [1.42 - 2.31]
> Warning: Large distance for BOND 26 O6 K 0 2.86 [1.42 - 2.31]
> Warning: Large distance for BOND 27 O6 K 0 2.91 [1.42 - 2.31]
> Warning: Large distance for BOND 28 O6 K 0 2.71 [1.42 - 2.31]
> Warning: Large distance for BOND 49 O6 K 0 2.65 [1.42 - 2.31]
> Warning: Large distance for BOND 50 O6 K 0 2.72 [1.42 - 2.31]
> Warning: Large distance for BOND 51 O6 K 0 3.00 [1.42 - 2.31]
> Warning: Large distance for BOND 52 O6 K 0 2.64 [1.42 - 2.31]
> Warning: Large distance for BOND 53 O6 K 0 2.69 [1.42 - 2.31]
> Warning: Large distance for BOND 54 O6 K 0 2.71 [1.42 - 2.31]
> Warning: Large distance for BOND 55 O6 K 0 3.12 [1.42 - 2.31]
> Warning: Large distance for BOND 56 O6 K 0 2.69 [1.42 - 2.31]
> for those not bonded
> Warning: Close ( 1.47) nonbonded atoms (ID: 19, Name: P) and (ID: 20,
> Name: OP1).
> Warning: Close ( 1.47) nonbonded atoms (ID: 19, Name: P) and (ID: 21,
> Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 19, Name: P) and (ID: 22,
> Name: O5').
> Warning: Close ( 1.37) nonbonded atoms (ID: 22, Name: O5') and (ID:
> 23, Name: C5').
> Warning: Close ( 1.51) nonbonded atoms (ID: 23, Name: C5') and (ID:
> 24, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 24, Name: C4') and (ID:
> 25, Name: O4').
> Warning: Close ( 1.52) nonbonded atoms (ID: 24, Name: C4') and (ID:
> 26, Name: C3').
> Warning: Close ( 1.42) nonbonded atoms (ID: 25, Name: O4') and (ID:
> 30, Name: C1').
> Warning: Close ( 1.43) nonbonded atoms (ID: 26, Name: C3') and (ID:
> 27, Name: O3').
> Warning: Close ( 1.51) nonbonded atoms (ID: 26, Name: C3') and (ID:
> 28, Name: C2').
> Warning: Close ( 1.61) nonbonded atoms (ID: 27, Name: O3') and (ID:
> 41, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 28, Name: C2') and (ID:
> 29, Name: O2').
> Warning: Close ( 1.52) nonbonded atoms (ID: 28, Name: C2') and (ID:
> 30, Name: C1').
> Warning: Close ( 1.48) nonbonded atoms (ID: 30, Name: C1') and (ID:
> 31, Name: N9).
> Warning: Close ( 1.38) nonbonded atoms (ID: 31, Name: N9) and (ID: 32,
> Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 31, Name: N9) and (ID: 40,
> Name: C4).
> Warning: Close ( 1.32) nonbonded atoms (ID: 32, Name: C8) and (ID: 33,
> Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 33, Name: N7) and (ID: 34,
> Name: C5).
> Warning: Close ( 1.40) nonbonded atoms (ID: 34, Name: C5) and (ID: 35,
> Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 34, Name: C5) and (ID: 40,
> Name: C4).
> Warning: Close ( 1.32) nonbonded atoms (ID: 35, Name: C6) and (ID: 36,
> Name: N6).
> Warning: Close ( 1.33) nonbonded atoms (ID: 35, Name: C6) and (ID: 37,
> Name: N1).
> Warning: Close ( 1.33) nonbonded atoms (ID: 37, Name: N1) and (ID: 38,
> Name: C2).
> Warning: Close ( 1.33) nonbonded atoms (ID: 38, Name: C2) and (ID: 39,
> Name: N3).
> Warning: Close ( 1.34) nonbonded atoms (ID: 39, Name: N3) and (ID: 40,
> Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 41, Name: P) and (ID: 42,
> Name: OP1).
> Warning: Close ( 1.49) nonbonded atoms (ID: 41, Name: P) and (ID: 43,
> Name: OP2).
> Warning: Close ( 1.59) nonbonded atoms (ID: 41, Name: P) and (ID: 44,
> Name: O5').
> Warning: Close ( 1.41) nonbonded atoms (ID: 44, Name: O5') and (ID:
> 45, Name: C5').
> Warning: Close ( 1.51) nonbonded atoms (ID: 45, Name: C5') and (ID:
> 46, Name: C4').
> Warning: Close ( 1.47) nonbonded atoms (ID: 46, Name: C4') and (ID:
> 47, Name: O4').
> Warning: Close ( 1.55) nonbonded atoms (ID: 46, Name: C4') and (ID:
> 48, Name: C3').
> Warning: Close ( 1.40) nonbonded atoms (ID: 47, Name: O4') and (ID:
> 52, Name: C1').
> Warning: Close ( 1.45) nonbonded atoms (ID: 48, Name: C3') and (ID:
> 49, Name: O3').
> Warning: Close ( 1.50) nonbonded atoms (ID: 48, Name: C3') and (ID:
> 50, Name: C2').
> Warning: Close ( 1.62) nonbonded atoms (ID: 49, Name: O3') and (ID:
> 64, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 50, Name: C2') and (ID:
> 51, Name: O2').
> Warning: Close ( 1.54) nonbonded atoms (ID: 50, Name: C2') and (ID:
> 52, Name: C1').
> Warning: Close ( 1.47) nonbonded atoms (ID: 52, Name: C1') and (ID:
> 53, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 53, Name: N9) and (ID: 54,
> Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 53, Name: N9) and (ID: 63,
> Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 54, Name: C8) and (ID: 55,
> Name: N7).
> Warning: Close ( 1.38) nonbonded atoms (ID: 55, Name: N7) and (ID: 56,
> Name: C5).
> Warning: Close ( 1.41) nonbonded atoms (ID: 56, Name: C5) and (ID: 57,
> Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 56, Name: C5) and (ID: 63,
> Name: C4).
> Warning: Close ( 1.24) nonbonded atoms (ID: 57, Name: C6) and (ID: 58,
> Name: O6).
> Warning: Close ( 1.40) nonbonded atoms (ID: 57, Name: C6) and (ID: 59,
> Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 59, Name: N1) and (ID: 60,
> Name: C2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 60, Name: C2) and (ID: 61,
> Name: N2).
> Warning: Close ( 1.32) nonbonded atoms (ID: 60, Name: C2) and (ID: 62,
> Name: N3).
> Warning: Close ( 1.37) nonbonded atoms (ID: 62, Name: N3) and (ID: 63,
> Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 64, Name: P) and (ID: 65,
> Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 64, Name: P) and (ID: 66,
> Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 64, Name: P) and (ID: 67,
> Name: O5').
> Warning: Close ( 1.39) nonbonded atoms (ID: 67, Name: O5') and (ID:
> 68, Name: C5').
> Warning: Close ( 1.51) nonbonded atoms (ID: 68, Name: C5') and (ID:
> 69, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 69, Name: C4') and (ID:
> 70, Name: O4').
> Warning: Close ( 1.52) nonbonded atoms (ID: 69, Name: C4') and (ID:
> 71, Name: C3').
> Warning: Close ( 1.42) nonbonded atoms (ID: 70, Name: O4') and (ID:
> 75, Name: C1').
> Warning: Close ( 1.41) nonbonded atoms (ID: 71, Name: C3') and (ID:
> 72, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 71, Name: C3') and (ID:
> 73, Name: C2').
> Warning: Close ( 1.59) nonbonded atoms (ID: 72, Name: O3') and (ID:
> 87, Name: P).
> Warning: Close ( 1.43) nonbonded atoms (ID: 73, Name: C2') and (ID:
> 74, Name: O2').
> Warning: Close ( 1.53) nonbonded atoms (ID: 73, Name: C2') and (ID:
> 75, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 75, Name: C1') and (ID:
> 76, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 76, Name: N9) and (ID: 77,
> Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 76, Name: N9) and (ID: 86,
> Name: C4).
> Warning: Close ( 1.32) nonbonded atoms (ID: 77, Name: C8) and (ID: 78,
> Name: N7).
> Warning: Close ( 1.39) nonbonded atoms (ID: 78, Name: N7) and (ID: 79,
> Name: C5).
> Warning: Close ( 1.41) nonbonded atoms (ID: 79, Name: C5) and (ID: 80,
> Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 79, Name: C5) and (ID: 86,
> Name: C4).
> Warning: Close ( 1.24) nonbonded atoms (ID: 80, Name: C6) and (ID: 81,
> Name: O6).
> Warning: Close ( 1.39) nonbonded atoms (ID: 80, Name: C6) and (ID: 82,
> Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 82, Name: N1) and (ID: 83,
> Name: C2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 83, Name: C2) and (ID: 84,
> Name: N2).
> Warning: Close ( 1.32) nonbonded atoms (ID: 83, Name: C2) and (ID: 85,
> Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 85, Name: N3) and (ID: 86,
> Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 87, Name: P) and (ID: 88,
> Name: OP1).
> Warning: Close ( 1.47) nonbonded atoms (ID: 87, Name: P) and (ID: 89,
> Name: OP2).
> Warning: Close ( 1.59) nonbonded atoms (ID: 87, Name: P) and (ID: 90,
> Name: O5').
> Warning: Close ( 1.42) nonbonded atoms (ID: 90, Name: O5') and (ID:
> 91, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 91, Name: C5') and (ID:
> 92, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 92, Name: C4') and (ID:
> 93, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 92, Name: C4') and (ID:
> 94, Name: C3').
> Warning: Close ( 1.39) nonbonded atoms (ID: 93, Name: O4') and (ID:
> 98, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 94, Name: C3') and (ID:
> 95, Name: O3').
> Warning: Close ( 1.50) nonbonded atoms (ID: 94, Name: C3') and (ID:
> 96, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 95, Name: O3') and (ID:
> 110, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 96, Name: C2') and (ID:
> 97, Name: O2').
> Warning: Close ( 1.53) nonbonded atoms (ID: 96, Name: C2') and (ID:
> 98, Name: C1').
> Warning: Close ( 1.47) nonbonded atoms (ID: 98, Name: C1') and (ID:
> 99, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 99, Name: N9) and (ID:
> 100, Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 99, Name: N9) and (ID:
> 109, Name: C4).
> Warning: Close ( 1.29) nonbonded atoms (ID: 100, Name: C8) and (ID:
> 101, Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 101, Name: N7) and (ID:
> 102, Name: C5).
> Warning: Close ( 1.42) nonbonded atoms (ID: 102, Name: C5) and (ID:
> 103, Name: C6).
> Warning: Close ( 1.36) nonbonded atoms (ID: 102, Name: C5) and (ID:
> 109, Name: C4).
> Warning: Close ( 1.24) nonbonded atoms (ID: 103, Name: C6) and (ID:
> 104, Name: O6).
> Warning: Close ( 1.40) nonbonded atoms (ID: 103, Name: C6) and (ID:
> 105, Name: N1).
> Warning: Close ( 1.37) nonbonded atoms (ID: 105, Name: N1) and (ID:
> 106, Name: C2).
> Warning: Close ( 1.36) nonbonded atoms (ID: 106, Name: C2) and (ID:
> 107, Name: N2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 106, Name: C2) and (ID:
> 108, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 108, Name: N3) and (ID:
> 109, Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 110, Name: P) and (ID:
> 111, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 110, Name: P) and (ID:
> 112, Name: OP2).
> Warning: Close ( 1.56) nonbonded atoms (ID: 110, Name: P) and (ID:
> 113, Name: O5').
> Warning: Close ( 1.37) nonbonded atoms (ID: 113, Name: O5') and (ID:
> 114, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 114, Name: C5') and (ID:
> 115, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 115, Name: C4') and (ID:
> 116, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 115, Name: C4') and (ID:
> 117, Name: C3').
> Warning: Close ( 1.39) nonbonded atoms (ID: 116, Name: O4') and (ID:
> 121, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 117, Name: C3') and (ID:
> 118, Name: O3').
> Warning: Close ( 1.55) nonbonded atoms (ID: 117, Name: C3') and (ID:
> 119, Name: C2').
> Warning: Close ( 1.61) nonbonded atoms (ID: 118, Name: O3') and (ID:
> 130, Name: P).
> Warning: Close ( 1.40) nonbonded atoms (ID: 119, Name: C2') and (ID:
> 120, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 119, Name: C2') and (ID:
> 121, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 121, Name: C1') and (ID:
> 122, Name: N1).
> Warning: Close ( 1.39) nonbonded atoms (ID: 122, Name: N1) and (ID:
> 123, Name: C2).
> Warning: Close ( 1.38) nonbonded atoms (ID: 122, Name: N1) and (ID:
> 129, Name: C6).
> Warning: Close ( 1.22) nonbonded atoms (ID: 123, Name: C2) and (ID:
> 124, Name: O2).
> Warning: Close ( 1.36) nonbonded atoms (ID: 123, Name: C2) and (ID:
> 125, Name: N3).
> Warning: Close ( 1.37) nonbonded atoms (ID: 125, Name: N3) and (ID:
> 126, Name: C4).
> Warning: Close ( 1.20) nonbonded atoms (ID: 126, Name: C4) and (ID:
> 127, Name: O4).
> Warning: Close ( 1.43) nonbonded atoms (ID: 126, Name: C4) and (ID:
> 128, Name: C5).
> Warning: Close ( 1.32) nonbonded atoms (ID: 128, Name: C5) and (ID:
> 129, Name: C6).
> Warning: Close ( 1.48) nonbonded atoms (ID: 130, Name: P) and (ID:
> 131, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 130, Name: P) and (ID:
> 132, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 130, Name: P) and (ID:
> 133, Name: O5').
> Warning: Close ( 1.41) nonbonded atoms (ID: 133, Name: O5') and (ID:
> 134, Name: C5').
> Warning: Close ( 1.52) nonbonded atoms (ID: 134, Name: C5') and (ID:
> 135, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 135, Name: C4') and (ID:
> 136, Name: O4').
> Warning: Close ( 1.52) nonbonded atoms (ID: 135, Name: C4') and (ID:
> 137, Name: C3').
> Warning: Close ( 1.43) nonbonded atoms (ID: 136, Name: O4') and (ID:
> 141, Name: C1').
> Warning: Close ( 1.40) nonbonded atoms (ID: 137, Name: C3') and (ID:
> 138, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 137, Name: C3') and (ID:
> 139, Name: C2').
> Warning: Close ( 1.61) nonbonded atoms (ID: 138, Name: O3') and (ID:
> 150, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 139, Name: C2') and (ID:
> 140, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 139, Name: C2') and (ID:
> 141, Name: C1').
> Warning: Close ( 1.50) nonbonded atoms (ID: 141, Name: C1') and (ID:
> 142, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 142, Name: N1) and (ID:
> 143, Name: C2).
> Warning: Close ( 1.38) nonbonded atoms (ID: 142, Name: N1) and (ID:
> 149, Name: C6).
> Warning: Close ( 1.22) nonbonded atoms (ID: 143, Name: C2) and (ID:
> 144, Name: O2).
> Warning: Close ( 1.37) nonbonded atoms (ID: 143, Name: C2) and (ID:
> 145, Name: N3).
> Warning: Close ( 1.39) nonbonded atoms (ID: 145, Name: N3) and (ID:
> 146, Name: C4).
> Warning: Close ( 1.23) nonbonded atoms (ID: 146, Name: C4) and (ID:
> 147, Name: O4).
> Warning: Close ( 1.44) nonbonded atoms (ID: 146, Name: C4) and (ID:
> 148, Name: C5).
> Warning: Close ( 1.34) nonbonded atoms (ID: 148, Name: C5) and (ID:
> 149, Name: C6).
> Warning: Close ( 1.48) nonbonded atoms (ID: 150, Name: P) and (ID:
> 151, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 150, Name: P) and (ID:
> 152, Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 150, Name: P) and (ID:
> 153, Name: O5').
> Warning: Close ( 1.40) nonbonded atoms (ID: 153, Name: O5') and (ID:
> 154, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 154, Name: C5') and (ID:
> 155, Name: C4').
> Warning: Close ( 1.46) nonbonded atoms (ID: 155, Name: C4') and (ID:
> 156, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 155, Name: C4') and (ID:
> 157, Name: C3').
> Warning: Close ( 1.39) nonbonded atoms (ID: 156, Name: O4') and (ID:
> 161, Name: C1').
> Warning: Close ( 1.40) nonbonded atoms (ID: 157, Name: C3') and (ID:
> 158, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 157, Name: C3') and (ID:
> 159, Name: C2').
> Warning: Close ( 1.57) nonbonded atoms (ID: 158, Name: O3') and (ID:
> 172, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 159, Name: C2') and (ID:
> 160, Name: O2').
> Warning: Close ( 1.52) nonbonded atoms (ID: 159, Name: C2') and (ID:
> 161, Name: C1').
> Warning: Close ( 1.45) nonbonded atoms (ID: 161, Name: C1') and (ID:
> 162, Name: N9).
> Warning: Close ( 1.36) nonbonded atoms (ID: 162, Name: N9) and (ID:
> 163, Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 162, Name: N9) and (ID:
> 171, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 163, Name: C8) and (ID:
> 164, Name: N7).
> Warning: Close ( 1.39) nonbonded atoms (ID: 164, Name: N7) and (ID:
> 165, Name: C5).
> Warning: Close ( 1.42) nonbonded atoms (ID: 165, Name: C5) and (ID:
> 166, Name: C6).
> Warning: Close ( 1.37) nonbonded atoms (ID: 165, Name: C5) and (ID:
> 171, Name: C4).
> Warning: Close ( 1.33) nonbonded atoms (ID: 166, Name: C6) and (ID:
> 167, Name: N6).
> Warning: Close ( 1.36) nonbonded atoms (ID: 166, Name: C6) and (ID:
> 168, Name: N1).
> Warning: Close ( 1.33) nonbonded atoms (ID: 168, Name: N1) and (ID:
> 169, Name: C2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 169, Name: C2) and (ID:
> 170, Name: N3).
> Warning: Close ( 1.35) nonbonded atoms (ID: 170, Name: N3) and (ID:
> 171, Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 172, Name: P) and (ID:
> 173, Name: OP1).
> Warning: Close ( 1.47) nonbonded atoms (ID: 172, Name: P) and (ID:
> 174, Name: OP2).
> Warning: Close ( 1.59) nonbonded atoms (ID: 172, Name: P) and (ID:
> 175, Name: O5').
> Warning: Close ( 1.37) nonbonded atoms (ID: 175, Name: O5') and (ID:
> 176, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 176, Name: C5') and (ID:
> 177, Name: C4').
> Warning: Close ( 1.45) nonbonded atoms (ID: 177, Name: C4') and (ID:
> 178, Name: O4').
> Warning: Close ( 1.54) nonbonded atoms (ID: 177, Name: C4') and (ID:
> 179, Name: C3').
> Warning: Close ( 1.39) nonbonded atoms (ID: 178, Name: O4') and (ID:
> 183, Name: C1').
> Warning: Close ( 1.43) nonbonded atoms (ID: 179, Name: C3') and (ID:
> 180, Name: O3').
> Warning: Close ( 1.49) nonbonded atoms (ID: 179, Name: C3') and (ID:
> 181, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 180, Name: O3') and (ID:
> 195, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 181, Name: C2') and (ID:
> 182, Name: O2').
> Warning: Close ( 1.54) nonbonded atoms (ID: 181, Name: C2') and (ID:
> 183, Name: C1').
> Warning: Close ( 1.45) nonbonded atoms (ID: 183, Name: C1') and (ID:
> 184, Name: N9).
> Warning: Close ( 1.38) nonbonded atoms (ID: 184, Name: N9) and (ID:
> 185, Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 184, Name: N9) and (ID:
> 194, Name: C4).
> Warning: Close ( 1.30) nonbonded atoms (ID: 185, Name: C8) and (ID:
> 186, Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 186, Name: N7) and (ID:
> 187, Name: C5).
> Warning: Close ( 1.40) nonbonded atoms (ID: 187, Name: C5) and (ID:
> 188, Name: C6).
> Warning: Close ( 1.37) nonbonded atoms (ID: 187, Name: C5) and (ID:
> 194, Name: C4).
> Warning: Close ( 1.22) nonbonded atoms (ID: 188, Name: C6) and (ID:
> 189, Name: O6).
> Warning: Close ( 1.39) nonbonded atoms (ID: 188, Name: C6) and (ID:
> 190, Name: N1).
> Warning: Close ( 1.36) nonbonded atoms (ID: 190, Name: N1) and (ID:
> 191, Name: C2).
> Warning: Close ( 1.35) nonbonded atoms (ID: 191, Name: C2) and (ID:
> 192, Name: N2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 191, Name: C2) and (ID:
> 193, Name: N3).
> Warning: Close ( 1.35) nonbonded atoms (ID: 193, Name: N3) and (ID:
> 194, Name: C4).
> Warning: Close ( 1.48) nonbonded atoms (ID: 195, Name: P) and (ID:
> 196, Name: OP1).
> Warning: Close ( 1.47) nonbonded atoms (ID: 195, Name: P) and (ID:
> 197, Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 195, Name: P) and (ID:
> 198, Name: O5').
> Warning: Close ( 1.38) nonbonded atoms (ID: 198, Name: O5') and (ID:
> 199, Name: C5').
> Warning: Close ( 1.49) nonbonded atoms (ID: 199, Name: C5') and (ID:
> 200, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 200, Name: C4') and (ID:
> 201, Name: O4').
> Warning: Close ( 1.51) nonbonded atoms (ID: 200, Name: C4') and (ID:
> 202, Name: C3').
> Warning: Close ( 1.41) nonbonded atoms (ID: 201, Name: O4') and (ID:
> 206, Name: C1').
> Warning: Close ( 1.44) nonbonded atoms (ID: 202, Name: C3') and (ID:
> 203, Name: O3').
> Warning: Close ( 1.53) nonbonded atoms (ID: 202, Name: C3') and (ID:
> 204, Name: C2').
> Warning: Close ( 1.62) nonbonded atoms (ID: 203, Name: O3') and (ID:
> 218, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 204, Name: C2') and (ID:
> 205, Name: O2').
> Warning: Close ( 1.52) nonbonded atoms (ID: 204, Name: C2') and (ID:
> 206, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 206, Name: C1') and (ID:
> 207, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 207, Name: N9) and (ID:
> 208, Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 207, Name: N9) and (ID:
> 217, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 208, Name: C8) and (ID:
> 209, Name: N7).
> Warning: Close ( 1.39) nonbonded atoms (ID: 209, Name: N7) and (ID:
> 210, Name: C5).
> Warning: Close ( 1.42) nonbonded atoms (ID: 210, Name: C5) and (ID:
> 211, Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 210, Name: C5) and (ID:
> 217, Name: C4).
> Warning: Close ( 1.24) nonbonded atoms (ID: 211, Name: C6) and (ID:
> 212, Name: O6).
> Warning: Close ( 1.40) nonbonded atoms (ID: 211, Name: C6) and (ID:
> 213, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 213, Name: N1) and (ID:
> 214, Name: C2).
> Warning: Close ( 1.35) nonbonded atoms (ID: 214, Name: C2) and (ID:
> 215, Name: N2).
> Warning: Close ( 1.33) nonbonded atoms (ID: 214, Name: C2) and (ID:
> 216, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 216, Name: N3) and (ID:
> 217, Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 218, Name: P) and (ID:
> 219, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 218, Name: P) and (ID:
> 220, Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 218, Name: P) and (ID:
> 221, Name: O5').
> Warning: Close ( 1.41) nonbonded atoms (ID: 221, Name: O5') and (ID:
> 222, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 222, Name: C5') and (ID:
> 223, Name: C4').
> Warning: Close ( 1.45) nonbonded atoms (ID: 223, Name: C4') and (ID:
> 224, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 223, Name: C4') and (ID:
> 225, Name: C3').
> Warning: Close ( 1.43) nonbonded atoms (ID: 224, Name: O4') and (ID:
> 229, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 225, Name: C3') and (ID:
> 226, Name: O3').
> Warning: Close ( 1.53) nonbonded atoms (ID: 225, Name: C3') and (ID:
> 227, Name: C2').
> Warning: Close ( 1.59) nonbonded atoms (ID: 226, Name: O3') and (ID:
> 241, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 227, Name: C2') and (ID:
> 228, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 227, Name: C2') and (ID:
> 229, Name: C1').
> Warning: Close ( 1.44) nonbonded atoms (ID: 229, Name: C1') and (ID:
> 230, Name: N9).
> Warning: Close ( 1.38) nonbonded atoms (ID: 230, Name: N9) and (ID:
> 231, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 230, Name: N9) and (ID:
> 240, Name: C4).
> Warning: Close ( 1.29) nonbonded atoms (ID: 231, Name: C8) and (ID:
> 232, Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 232, Name: N7) and (ID:
> 233, Name: C5).
> Warning: Close ( 1.41) nonbonded atoms (ID: 233, Name: C5) and (ID:
> 234, Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 233, Name: C5) and (ID:
> 240, Name: C4).
> Warning: Close ( 1.25) nonbonded atoms (ID: 234, Name: C6) and (ID:
> 235, Name: O6).
> Warning: Close ( 1.39) nonbonded atoms (ID: 234, Name: C6) and (ID:
> 236, Name: N1).
> Warning: Close ( 1.37) nonbonded atoms (ID: 236, Name: N1) and (ID:
> 237, Name: C2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 237, Name: C2) and (ID:
> 238, Name: N2).
> Warning: Close ( 1.33) nonbonded atoms (ID: 237, Name: C2) and (ID:
> 239, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 239, Name: N3) and (ID:
> 240, Name: C4).
> Warning: Close ( 1.49) nonbonded atoms (ID: 241, Name: P) and (ID:
> 242, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 241, Name: P) and (ID:
> 243, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 241, Name: P) and (ID:
> 244, Name: O5').
> Warning: Close ( 1.53) nonbonded atoms (ID: 244, Name: O5') and (ID:
> 245, Name: C5').
> Warning: Close ( 1.52) nonbonded atoms (ID: 245, Name: C5') and (ID:
> 246, Name: C4').
> Warning: Close ( 1.45) nonbonded atoms (ID: 246, Name: C4') and (ID:
> 247, Name: O4').
> Warning: Close ( 1.54) nonbonded atoms (ID: 246, Name: C4') and (ID:
> 248, Name: C3').
> Warning: Close ( 1.40) nonbonded atoms (ID: 247, Name: O4') and (ID:
> 252, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 248, Name: C3') and (ID:
> 249, Name: O3').
> Warning: Close ( 1.53) nonbonded atoms (ID: 248, Name: C3') and (ID:
> 250, Name: C2').
> Warning: Close ( 1.41) nonbonded atoms (ID: 250, Name: C2') and (ID:
> 251, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 250, Name: C2') and (ID:
> 252, Name: C1').
> Warning: Close ( 1.48) nonbonded atoms (ID: 252, Name: C1') and (ID:
> 253, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 253, Name: N1) and (ID:
> 254, Name: C2).
> Warning: Close ( 1.38) nonbonded atoms (ID: 253, Name: N1) and (ID:
> 260, Name: C6).
> Warning: Close ( 1.22) nonbonded atoms (ID: 254, Name: C2) and (ID:
> 255, Name: O2).
> Warning: Close ( 1.37) nonbonded atoms (ID: 254, Name: C2) and (ID:
> 256, Name: N3).
> Warning: Close ( 1.38) nonbonded atoms (ID: 256, Name: N3) and (ID:
> 257, Name: C4).
> Warning: Close ( 1.23) nonbonded atoms (ID: 257, Name: C4) and (ID:
> 258, Name: O4).
> Warning: Close ( 1.44) nonbonded atoms (ID: 257, Name: C4) and (ID:
> 259, Name: C5).
> Warning: Close ( 1.34) nonbonded atoms (ID: 259, Name: C5) and (ID:
> 260, Name: C6).
> Warning: Close ( 1.47) nonbonded atoms (ID: 279, Name: P) and (ID:
> 280, Name: OP1).
> Warning: Close ( 1.46) nonbonded atoms (ID: 279, Name: P) and (ID:
> 281, Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 279, Name: P) and (ID:
> 282, Name: O5').
> Warning: Close ( 1.42) nonbonded atoms (ID: 282, Name: O5') and (ID:
> 283, Name: C5').
> Warning: Close ( 1.51) nonbonded atoms (ID: 283, Name: C5') and (ID:
> 284, Name: C4').
> Warning: Close ( 1.43) nonbonded atoms (ID: 284, Name: C4') and (ID:
> 285, Name: O4').
> Warning: Close ( 1.51) nonbonded atoms (ID: 284, Name: C4') and (ID:
> 286, Name: C3').
> Warning: Close ( 1.43) nonbonded atoms (ID: 285, Name: O4') and (ID:
> 290, Name: C1').
> Warning: Close ( 1.40) nonbonded atoms (ID: 286, Name: C3') and (ID:
> 287, Name: O3').
> Warning: Close ( 1.51) nonbonded atoms (ID: 286, Name: C3') and (ID:
> 288, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 287, Name: O3') and (ID:
> 301, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 288, Name: C2') and (ID:
> 289, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 288, Name: C2') and (ID:
> 290, Name: C1').
> Warning: Close ( 1.45) nonbonded atoms (ID: 290, Name: C1') and (ID:
> 291, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 291, Name: N9) and (ID:
> 292, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 291, Name: N9) and (ID:
> 300, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 292, Name: C8) and (ID:
> 293, Name: N7).
> Warning: Close ( 1.39) nonbonded atoms (ID: 293, Name: N7) and (ID:
> 294, Name: C5).
> Warning: Close ( 1.40) nonbonded atoms (ID: 294, Name: C5) and (ID:
> 295, Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 294, Name: C5) and (ID:
> 300, Name: C4).
> Warning: Close ( 1.33) nonbonded atoms (ID: 295, Name: C6) and (ID:
> 296, Name: N6).
> Warning: Close ( 1.34) nonbonded atoms (ID: 295, Name: C6) and (ID:
> 297, Name: N1).
> Warning: Close ( 1.34) nonbonded atoms (ID: 297, Name: N1) and (ID:
> 298, Name: C2).
> Warning: Close ( 1.32) nonbonded atoms (ID: 298, Name: C2) and (ID:
> 299, Name: N3).
> Warning: Close ( 1.34) nonbonded atoms (ID: 299, Name: N3) and (ID:
> 300, Name: C4).
> Warning: Close ( 1.46) nonbonded atoms (ID: 301, Name: P) and (ID:
> 302, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 301, Name: P) and (ID:
> 303, Name: OP2).
> Warning: Close ( 1.57) nonbonded atoms (ID: 301, Name: P) and (ID:
> 304, Name: O5').
> Warning: Close ( 1.38) nonbonded atoms (ID: 304, Name: O5') and (ID:
> 305, Name: C5').
> Warning: Close ( 1.49) nonbonded atoms (ID: 305, Name: C5') and (ID:
> 306, Name: C4').
> Warning: Close ( 1.42) nonbonded atoms (ID: 306, Name: C4') and (ID:
> 307, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 306, Name: C4') and (ID:
> 308, Name: C3').
> Warning: Close ( 1.40) nonbonded atoms (ID: 307, Name: O4') and (ID:
> 312, Name: C1').
> Warning: Close ( 1.40) nonbonded atoms (ID: 308, Name: C3') and (ID:
> 309, Name: O3').
> Warning: Close ( 1.53) nonbonded atoms (ID: 308, Name: C3') and (ID:
> 310, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 309, Name: O3') and (ID:
> 324, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 310, Name: C2') and (ID:
> 311, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 310, Name: C2') and (ID:
> 312, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 312, Name: C1') and (ID:
> 313, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 313, Name: N9) and (ID:
> 314, Name: C8).
> Warning: Close ( 1.36) nonbonded atoms (ID: 313, Name: N9) and (ID:
> 323, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 314, Name: C8) and (ID:
> 315, Name: N7).
> Warning: Close ( 1.39) nonbonded atoms (ID: 315, Name: N7) and (ID:
> 316, Name: C5).
> Warning: Close ( 1.40) nonbonded atoms (ID: 316, Name: C5) and (ID:
> 317, Name: C6).
> Warning: Close ( 1.37) nonbonded atoms (ID: 316, Name: C5) and (ID:
> 323, Name: C4).
> Warning: Close ( 1.23) nonbonded atoms (ID: 317, Name: C6) and (ID:
> 318, Name: O6).
> Warning: Close ( 1.39) nonbonded atoms (ID: 317, Name: C6) and (ID:
> 319, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 319, Name: N1) and (ID:
> 320, Name: C2).
> Warning: Close ( 1.35) nonbonded atoms (ID: 320, Name: C2) and (ID:
> 321, Name: N2).
> Warning: Close ( 1.31) nonbonded atoms (ID: 320, Name: C2) and (ID:
> 322, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 322, Name: N3) and (ID:
> 323, Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 324, Name: P) and (ID:
> 325, Name: OP1).
> Warning: Close ( 1.49) nonbonded atoms (ID: 324, Name: P) and (ID:
> 326, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 324, Name: P) and (ID:
> 327, Name: O5').
> Warning: Close ( 1.39) nonbonded atoms (ID: 327, Name: O5') and (ID:
> 328, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 328, Name: C5') and (ID:
> 329, Name: C4').
> Warning: Close ( 1.43) nonbonded atoms (ID: 329, Name: C4') and (ID:
> 330, Name: O4').
> Warning: Close ( 1.49) nonbonded atoms (ID: 329, Name: C4') and (ID:
> 331, Name: C3').
> Warning: Close ( 1.43) nonbonded atoms (ID: 330, Name: O4') and (ID:
> 335, Name: C1').
> Warning: Close ( 1.39) nonbonded atoms (ID: 331, Name: C3') and (ID:
> 332, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 331, Name: C3') and (ID:
> 333, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 332, Name: O3') and (ID:
> 347, Name: P).
> Warning: Close ( 1.40) nonbonded atoms (ID: 333, Name: C2') and (ID:
> 334, Name: O2').
> Warning: Close ( 1.52) nonbonded atoms (ID: 333, Name: C2') and (ID:
> 335, Name: C1').
> Warning: Close ( 1.47) nonbonded atoms (ID: 335, Name: C1') and (ID:
> 336, Name: N9).
> Warning: Close ( 1.38) nonbonded atoms (ID: 336, Name: N9) and (ID:
> 337, Name: C8).
> Warning: Close ( 1.38) nonbonded atoms (ID: 336, Name: N9) and (ID:
> 346, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 337, Name: C8) and (ID:
> 338, Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 338, Name: N7) and (ID:
> 339, Name: C5).
> Warning: Close ( 1.42) nonbonded atoms (ID: 339, Name: C5) and (ID:
> 340, Name: C6).
> Warning: Close ( 1.37) nonbonded atoms (ID: 339, Name: C5) and (ID:
> 346, Name: C4).
> Warning: Close ( 1.22) nonbonded atoms (ID: 340, Name: C6) and (ID:
> 341, Name: O6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 340, Name: C6) and (ID:
> 342, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 342, Name: N1) and (ID:
> 343, Name: C2).
> Warning: Close ( 1.35) nonbonded atoms (ID: 343, Name: C2) and (ID:
> 344, Name: N2).
> Warning: Close ( 1.33) nonbonded atoms (ID: 343, Name: C2) and (ID:
> 345, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 345, Name: N3) and (ID:
> 346, Name: C4).
> Warning: Close ( 1.48) nonbonded atoms (ID: 347, Name: P) and (ID:
> 348, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 347, Name: P) and (ID:
> 349, Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 347, Name: P) and (ID:
> 350, Name: O5').
> Warning: Close ( 1.42) nonbonded atoms (ID: 350, Name: O5') and (ID:
> 351, Name: C5').
> Warning: Close ( 1.51) nonbonded atoms (ID: 351, Name: C5') and (ID:
> 352, Name: C4').
> Warning: Close ( 1.46) nonbonded atoms (ID: 352, Name: C4') and (ID:
> 353, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 352, Name: C4') and (ID:
> 354, Name: C3').
> Warning: Close ( 1.41) nonbonded atoms (ID: 353, Name: O4') and (ID:
> 358, Name: C1').
> Warning: Close ( 1.41) nonbonded atoms (ID: 354, Name: C3') and (ID:
> 355, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 354, Name: C3') and (ID:
> 356, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 355, Name: O3') and (ID:
> 370, Name: P).
> Warning: Close ( 1.42) nonbonded atoms (ID: 356, Name: C2') and (ID:
> 357, Name: O2').
> Warning: Close ( 1.53) nonbonded atoms (ID: 356, Name: C2') and (ID:
> 358, Name: C1').
> Warning: Close ( 1.45) nonbonded atoms (ID: 358, Name: C1') and (ID:
> 359, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 359, Name: N9) and (ID:
> 360, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 359, Name: N9) and (ID:
> 369, Name: C4).
> Warning: Close ( 1.30) nonbonded atoms (ID: 360, Name: C8) and (ID:
> 361, Name: N7).
> Warning: Close ( 1.38) nonbonded atoms (ID: 361, Name: N7) and (ID:
> 362, Name: C5).
> Warning: Close ( 1.40) nonbonded atoms (ID: 362, Name: C5) and (ID:
> 363, Name: C6).
> Warning: Close ( 1.37) nonbonded atoms (ID: 362, Name: C5) and (ID:
> 369, Name: C4).
> Warning: Close ( 1.24) nonbonded atoms (ID: 363, Name: C6) and (ID:
> 364, Name: O6).
> Warning: Close ( 1.39) nonbonded atoms (ID: 363, Name: C6) and (ID:
> 365, Name: N1).
> Warning: Close ( 1.37) nonbonded atoms (ID: 365, Name: N1) and (ID:
> 366, Name: C2).
> Warning: Close ( 1.35) nonbonded atoms (ID: 366, Name: C2) and (ID:
> 367, Name: N2).
> Warning: Close ( 1.32) nonbonded atoms (ID: 366, Name: C2) and (ID:
> 368, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 368, Name: N3) and (ID:
> 369, Name: C4).
> Warning: Close ( 1.48) nonbonded atoms (ID: 370, Name: P) and (ID:
> 371, Name: OP1).
> Warning: Close ( 1.47) nonbonded atoms (ID: 370, Name: P) and (ID:
> 372, Name: OP2).
> Warning: Close ( 1.64) nonbonded atoms (ID: 370, Name: P) and (ID:
> 373, Name: O5').
> Warning: Close ( 1.43) nonbonded atoms (ID: 373, Name: O5') and (ID:
> 374, Name: C5').
> Warning: Close ( 1.52) nonbonded atoms (ID: 374, Name: C5') and (ID:
> 375, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 375, Name: C4') and (ID:
> 376, Name: O4').
> Warning: Close ( 1.53) nonbonded atoms (ID: 375, Name: C4') and (ID:
> 377, Name: C3').
> Warning: Close ( 1.40) nonbonded atoms (ID: 376, Name: O4') and (ID:
> 381, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 377, Name: C3') and (ID:
> 378, Name: O3').
> Warning: Close ( 1.54) nonbonded atoms (ID: 377, Name: C3') and (ID:
> 379, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 378, Name: O3') and (ID:
> 390, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 379, Name: C2') and (ID:
> 380, Name: O2').
> Warning: Close ( 1.52) nonbonded atoms (ID: 379, Name: C2') and (ID:
> 381, Name: C1').
> Warning: Close ( 1.49) nonbonded atoms (ID: 381, Name: C1') and (ID:
> 382, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 382, Name: N1) and (ID:
> 383, Name: C2).
> Warning: Close ( 1.38) nonbonded atoms (ID: 382, Name: N1) and (ID:
> 389, Name: C6).
> Warning: Close ( 1.22) nonbonded atoms (ID: 383, Name: C2) and (ID:
> 384, Name: O2).
> Warning: Close ( 1.37) nonbonded atoms (ID: 383, Name: C2) and (ID:
> 385, Name: N3).
> Warning: Close ( 1.38) nonbonded atoms (ID: 385, Name: N3) and (ID:
> 386, Name: C4).
> Warning: Close ( 1.23) nonbonded atoms (ID: 386, Name: C4) and (ID:
> 387, Name: O4).
> Warning: Close ( 1.44) nonbonded atoms (ID: 386, Name: C4) and (ID:
> 388, Name: C5).
> Warning: Close ( 1.34) nonbonded atoms (ID: 388, Name: C5) and (ID:
> 389, Name: C6).
> Warning: Close ( 1.48) nonbonded atoms (ID: 390, Name: P) and (ID:
> 391, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 390, Name: P) and (ID:
> 392, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 390, Name: P) and (ID:
> 393, Name: O5').
> Warning: Close ( 1.42) nonbonded atoms (ID: 393, Name: O5') and (ID:
> 394, Name: C5').
> Warning: Close ( 1.52) nonbonded atoms (ID: 394, Name: C5') and (ID:
> 395, Name: C4').
> Warning: Close ( 1.45) nonbonded atoms (ID: 395, Name: C4') and (ID:
> 396, Name: O4').
> Warning: Close ( 1.52) nonbonded atoms (ID: 395, Name: C4') and (ID:
> 397, Name: C3').
> Warning: Close ( 1.42) nonbonded atoms (ID: 396, Name: O4') and (ID:
> 401, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 397, Name: C3') and (ID:
> 398, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 397, Name: C3') and (ID:
> 399, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 398, Name: O3') and (ID:
> 410, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 399, Name: C2') and (ID:
> 400, Name: O2').
> Warning: Close ( 1.53) nonbonded atoms (ID: 399, Name: C2') and (ID:
> 401, Name: C1').
> Warning: Close ( 1.49) nonbonded atoms (ID: 401, Name: C1') and (ID:
> 402, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 402, Name: N1) and (ID:
> 403, Name: C2).
> Warning: Close ( 1.38) nonbonded atoms (ID: 402, Name: N1) and (ID:
> 409, Name: C6).
> Warning: Close ( 1.22) nonbonded atoms (ID: 403, Name: C2) and (ID:
> 404, Name: O2).
> Warning: Close ( 1.37) nonbonded atoms (ID: 403, Name: C2) and (ID:
> 405, Name: N3).
> Warning: Close ( 1.38) nonbonded atoms (ID: 405, Name: N3) and (ID:
> 406, Name: C4).
> Warning: Close ( 1.23) nonbonded atoms (ID: 406, Name: C4) and (ID:
> 407, Name: O4).
> Warning: Close ( 1.44) nonbonded atoms (ID: 406, Name: C4) and (ID:
> 408, Name: C5).
> Warning: Close ( 1.34) nonbonded atoms (ID: 408, Name: C5) and (ID:
> 409, Name: C6).
> Warning: Close ( 1.48) nonbonded atoms (ID: 410, Name: P) and (ID:
> 411, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 410, Name: P) and (ID:
> 412, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 410, Name: P) and (ID:
> 413, Name: O5').
> Warning: Close ( 1.43) nonbonded atoms (ID: 413, Name: O5') and (ID:
> 414, Name: C5').
> Warning: Close ( 1.52) nonbonded atoms (ID: 414, Name: C5') and (ID:
> 415, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 415, Name: C4') and (ID:
> 416, Name: O4').
> Warning: Close ( 1.54) nonbonded atoms (ID: 415, Name: C4') and (ID:
> 417, Name: C3').
> Warning: Close ( 1.39) nonbonded atoms (ID: 416, Name: O4') and (ID:
> 421, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 417, Name: C3') and (ID:
> 418, Name: O3').
> Warning: Close ( 1.54) nonbonded atoms (ID: 417, Name: C3') and (ID:
> 419, Name: C2').
> Warning: Close ( 1.61) nonbonded atoms (ID: 418, Name: O3') and (ID:
> 432, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 419, Name: C2') and (ID:
> 420, Name: O2').
> Warning: Close ( 1.52) nonbonded atoms (ID: 419, Name: C2') and (ID:
> 421, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 421, Name: C1') and (ID:
> 422, Name: N9).
> Warning: Close ( 1.37) nonbonded atoms (ID: 422, Name: N9) and (ID:
> 423, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 422, Name: N9) and (ID:
> 431, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 423, Name: C8) and (ID:
> 424, Name: N7).
> Warning: Close ( 1.39) nonbonded atoms (ID: 424, Name: N7) and (ID:
> 425, Name: C5).
> Warning: Close ( 1.41) nonbonded atoms (ID: 425, Name: C5) and (ID:
> 426, Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 425, Name: C5) and (ID:
> 431, Name: C4).
> Warning: Close ( 1.34) nonbonded atoms (ID: 426, Name: C6) and (ID:
> 427, Name: N6).
> Warning: Close ( 1.35) nonbonded atoms (ID: 426, Name: C6) and (ID:
> 428, Name: N1).
> Warning: Close ( 1.34) nonbonded atoms (ID: 428, Name: N1) and (ID:
> 429, Name: C2).
> Warning: Close ( 1.33) nonbonded atoms (ID: 429, Name: C2) and (ID:
> 430, Name: N3).
> Warning: Close ( 1.34) nonbonded atoms (ID: 430, Name: N3) and (ID:
> 431, Name: C4).
> Warning: Close ( 1.48) nonbonded atoms (ID: 432, Name: P) and (ID:
> 433, Name: OP1).
> Warning: Close ( 1.49) nonbonded atoms (ID: 432, Name: P) and (ID:
> 434, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 432, Name: P) and (ID:
> 435, Name: O5').
> Warning: Close ( 1.42) nonbonded atoms (ID: 435, Name: O5') and (ID:
> 436, Name: C5').
> Warning: Close ( 1.51) nonbonded atoms (ID: 436, Name: C5') and (ID:
> 437, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 437, Name: C4') and (ID:
> 438, Name: O4').
> Warning: Close ( 1.52) nonbonded atoms (ID: 437, Name: C4') and (ID:
> 439, Name: C3').
> Warning: Close ( 1.41) nonbonded atoms (ID: 438, Name: O4') and (ID:
> 443, Name: C1').
> Warning: Close ( 1.43) nonbonded atoms (ID: 439, Name: C3') and (ID:
> 440, Name: O3').
> Warning: Close ( 1.51) nonbonded atoms (ID: 439, Name: C3') and (ID:
> 441, Name: C2').
> Warning: Close ( 1.62) nonbonded atoms (ID: 440, Name: O3') and (ID:
> 455, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 441, Name: C2') and (ID:
> 442, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 441, Name: C2') and (ID:
> 443, Name: C1').
> Warning: Close ( 1.48) nonbonded atoms (ID: 443, Name: C1') and (ID:
> 444, Name: N9).
> Warning: Close ( 1.39) nonbonded atoms (ID: 444, Name: N9) and (ID:
> 445, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 444, Name: N9) and (ID:
> 454, Name: C4).
> Warning: Close ( 1.32) nonbonded atoms (ID: 445, Name: C8) and (ID:
> 446, Name: N7).
> Warning: Close ( 1.41) nonbonded atoms (ID: 446, Name: N7) and (ID:
> 447, Name: C5).
> Warning: Close ( 1.43) nonbonded atoms (ID: 447, Name: C5) and (ID:
> 448, Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 447, Name: C5) and (ID:
> 454, Name: C4).
> Warning: Close ( 1.25) nonbonded atoms (ID: 448, Name: C6) and (ID:
> 449, Name: O6).
> Warning: Close ( 1.39) nonbonded atoms (ID: 448, Name: C6) and (ID:
> 450, Name: N1).
> Warning: Close ( 1.39) nonbonded atoms (ID: 450, Name: N1) and (ID:
> 451, Name: C2).
> Warning: Close ( 1.35) nonbonded atoms (ID: 451, Name: C2) and (ID:
> 452, Name: N2).
> Warning: Close ( 1.31) nonbonded atoms (ID: 451, Name: C2) and (ID:
> 453, Name: N3).
> Warning: Close ( 1.35) nonbonded atoms (ID: 453, Name: N3) and (ID:
> 454, Name: C4).
> Warning: Close ( 1.48) nonbonded atoms (ID: 455, Name: P) and (ID:
> 456, Name: OP1).
> Warning: Close ( 1.50) nonbonded atoms (ID: 455, Name: P) and (ID:
> 457, Name: OP2).
> Warning: Close ( 1.58) nonbonded atoms (ID: 455, Name: P) and (ID:
> 458, Name: O5').
> Warning: Close ( 1.40) nonbonded atoms (ID: 458, Name: O5') and (ID:
> 459, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 459, Name: C5') and (ID:
> 460, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 460, Name: C4') and (ID:
> 461, Name: O4').
> Warning: Close ( 1.51) nonbonded atoms (ID: 460, Name: C4') and (ID:
> 462, Name: C3').
> Warning: Close ( 1.42) nonbonded atoms (ID: 461, Name: O4') and (ID:
> 466, Name: C1').
> Warning: Close ( 1.39) nonbonded atoms (ID: 462, Name: C3') and (ID:
> 463, Name: O3').
> Warning: Close ( 1.50) nonbonded atoms (ID: 462, Name: C3') and (ID:
> 464, Name: C2').
> Warning: Close ( 1.59) nonbonded atoms (ID: 463, Name: O3') and (ID:
> 478, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 464, Name: C2') and (ID:
> 465, Name: O2').
> Warning: Close ( 1.51) nonbonded atoms (ID: 464, Name: C2') and (ID:
> 466, Name: C1').
> Warning: Close ( 1.46) nonbonded atoms (ID: 466, Name: C1') and (ID:
> 467, Name: N9).
> Warning: Close ( 1.38) nonbonded atoms (ID: 467, Name: N9) and (ID:
> 468, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 467, Name: N9) and (ID:
> 477, Name: C4).
> Warning: Close ( 1.30) nonbonded atoms (ID: 468, Name: C8) and (ID:
> 469, Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 469, Name: N7) and (ID:
> 470, Name: C5).
> Warning: Close ( 1.43) nonbonded atoms (ID: 470, Name: C5) and (ID:
> 471, Name: C6).
> Warning: Close ( 1.37) nonbonded atoms (ID: 470, Name: C5) and (ID:
> 477, Name: C4).
> Warning: Close ( 1.25) nonbonded atoms (ID: 471, Name: C6) and (ID:
> 472, Name: O6).
> Warning: Close ( 1.40) nonbonded atoms (ID: 471, Name: C6) and (ID:
> 473, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 473, Name: N1) and (ID:
> 474, Name: C2).
> Warning: Close ( 1.34) nonbonded atoms (ID: 474, Name: C2) and (ID:
> 475, Name: N2).
> Warning: Close ( 1.33) nonbonded atoms (ID: 474, Name: C2) and (ID:
> 476, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 476, Name: N3) and (ID:
> 477, Name: C4).
> Warning: Close ( 1.47) nonbonded atoms (ID: 478, Name: P) and (ID:
> 479, Name: OP1).
> Warning: Close ( 1.48) nonbonded atoms (ID: 478, Name: P) and (ID:
> 480, Name: OP2).
> Warning: Close ( 1.57) nonbonded atoms (ID: 478, Name: P) and (ID:
> 481, Name: O5').
> Warning: Close ( 1.40) nonbonded atoms (ID: 481, Name: O5') and (ID:
> 482, Name: C5').
> Warning: Close ( 1.50) nonbonded atoms (ID: 482, Name: C5') and (ID:
> 483, Name: C4').
> Warning: Close ( 1.44) nonbonded atoms (ID: 483, Name: C4') and (ID:
> 484, Name: O4').
> Warning: Close ( 1.52) nonbonded atoms (ID: 483, Name: C4') and (ID:
> 485, Name: C3').
> Warning: Close ( 1.42) nonbonded atoms (ID: 484, Name: O4') and (ID:
> 489, Name: C1').
> Warning: Close ( 1.42) nonbonded atoms (ID: 485, Name: C3') and (ID:
> 486, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 485, Name: C3') and (ID:
> 487, Name: C2').
> Warning: Close ( 1.60) nonbonded atoms (ID: 486, Name: O3') and (ID:
> 501, Name: P).
> Warning: Close ( 1.41) nonbonded atoms (ID: 487, Name: C2') and (ID:
> 488, Name: O2').
> Warning: Close ( 1.53) nonbonded atoms (ID: 487, Name: C2') and (ID:
> 489, Name: C1').
> Warning: Close ( 1.45) nonbonded atoms (ID: 489, Name: C1') and (ID:
> 490, Name: N9).
> Warning: Close ( 1.39) nonbonded atoms (ID: 490, Name: N9) and (ID:
> 491, Name: C8).
> Warning: Close ( 1.37) nonbonded atoms (ID: 490, Name: N9) and (ID:
> 500, Name: C4).
> Warning: Close ( 1.31) nonbonded atoms (ID: 491, Name: C8) and (ID:
> 492, Name: N7).
> Warning: Close ( 1.40) nonbonded atoms (ID: 492, Name: N7) and (ID:
> 493, Name: C5).
> Warning: Close ( 1.41) nonbonded atoms (ID: 493, Name: C5) and (ID:
> 494, Name: C6).
> Warning: Close ( 1.38) nonbonded atoms (ID: 493, Name: C5) and (ID:
> 500, Name: C4).
> Warning: Close ( 1.24) nonbonded atoms (ID: 494, Name: C6) and (ID:
> 495, Name: O6).
> Warning: Close ( 1.41) nonbonded atoms (ID: 494, Name: C6) and (ID:
> 496, Name: N1).
> Warning: Close ( 1.39) nonbonded atoms (ID: 496, Name: N1) and (ID:
> 497, Name: C2).
> Warning: Close ( 1.36) nonbonded atoms (ID: 497, Name: C2) and (ID:
> 498, Name: N2).
> Warning: Close ( 1.32) nonbonded atoms (ID: 497, Name: C2) and (ID:
> 499, Name: N3).
> Warning: Close ( 1.36) nonbonded atoms (ID: 499, Name: N3) and (ID:
> 500, Name: C4).
> Warning: Close ( 1.48) nonbonded atoms (ID: 501, Name: P) and (ID:
> 502, Name: OP1).
> Warning: Close ( 1.47) nonbonded atoms (ID: 501, Name: P) and (ID:
> 503, Name: OP2).
> Warning: Close ( 1.60) nonbonded atoms (ID: 501, Name: P) and (ID:
> 504, Name: O5').
> Warning: Close ( 1.42) nonbonded atoms (ID: 504, Name: O5') and (ID:
> 505, Name: C5').
> Warning: Close ( 1.53) nonbonded atoms (ID: 505, Name: C5') and (ID:
> 506, Name: C4').
> Warning: Close ( 1.47) nonbonded atoms (ID: 506, Name: C4') and (ID:
> 507, Name: O4').
> Warning: Close ( 1.54) nonbonded atoms (ID: 506, Name: C4') and (ID:
> 508, Name: C3').
> Warning: Close ( 1.42) nonbonded atoms (ID: 507, Name: O4') and (ID:
> 512, Name: C1').
> Warning: Close ( 1.41) nonbonded atoms (ID: 508, Name: C3') and (ID:
> 509, Name: O3').
> Warning: Close ( 1.52) nonbonded atoms (ID: 508, Name: C3') and (ID:
> 510, Name: C2').
> Warning: Close ( 1.42) nonbonded atoms (ID: 510, Name: C2') and (ID:
> 511, Name: O2').
> Warning: Close ( 1.53) nonbonded atoms (ID: 510, Name: C2') and (ID:
> 512, Name: C1').
> Warning: Close ( 1.50) nonbonded atoms (ID: 512, Name: C1') and (ID:
> 513, Name: N1).
> Warning: Close ( 1.38) nonbonded atoms (ID: 513, Name: N1) and (ID:
> 514, Name: C2).
> Warning: Close ( 1.39) nonbonded atoms (ID: 513, Name: N1) and (ID:
> 520, Name: C6).
> Warning: Close ( 1.22) nonbonded atoms (ID: 514, Name: C2) and (ID:
> 515, Name: O2).
> Warning: Close ( 1.39) nonbonded atoms (ID: 514, Name: C2) and (ID:
> 516, Name: N3).
> Warning: Close ( 1.39) nonbonded atoms (ID: 516, Name: N3) and (ID:
> 517, Name: C4).
> Warning: Close ( 1.22) nonbonded atoms (ID: 517, Name: C4) and (ID:
> 518, Name: O4).
> Warning: Close ( 1.44) nonbonded atoms (ID: 517, Name: C4) and (ID:
> 519, Name: C5).
> Warning: Close ( 1.34) nonbonded atoms (ID: 519, Name: C5) and (ID:
> 520, Name: C6).
> -- Check Weird Bonds --
> /home/Applications/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
> Number of bonded atoms (7) for atom (ID: 521, Name: K) exceeds 6.
> antechamber cannot handle such kinds of molecules.
>
> Can you give me some advice?
> p.s. I am a beginner in the field, so please take it into account
> while explaining something
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Nov 14 2017 - 10:00:03 PST