Dear All (and David),
I think tleap residues start with 0, but in the pdb/prmtop-rst7 it writes
first residue as 1.
Assuming this is correct, I changed residue numbers in the bond commands
given to tleap and then read the prmtop/rst7 files in parmed and asked it
to printbonds :420,482 and printbonds :421,482 (shown below).
The output doesn't contain very large bonds (but some are < 0.7A and thus
high E), I hope minimization can fix this. (tleap terminal output is given
at the end; there is still a warning about 4A bond, which doesn't seem to
be coming from non-standard CYS-HEM, but not sure what/where is this long
bond still hiding!).
So parmed shows that the bond are there, but *I still can't see them in vmd*.
But strangely, the terminal OXT atom is still present, do I need to
explicitly delete it? Should it not get deleted when I bond the residue to
another standard/non-standard ones?
I think the fact that terminal OXT and NH atoms for 420, 421 are still
there is a problem and needs fixing before regular MD (min, heat, equil)
jobs can be started.
Please suggest on these aspects and any other issue that I may have missed
out.
Thank you very much.
(base) [exx.c107739 xleap-mol2]$ parmed -p com1.prmtop -c com1.rst7
____ .---. ,-----. _____
.' `,.': :'' : :.' `.
| : : ' ' ' ' : : \
| ' ' ' ' \
| v \
| | v \
| | | v \
| P | A | R | M | \
| | | | | \
| | | | | \
| | | | | \
| ===== | | | | )
\ --- /| ===== | | | /
`---' \ --- /| ===== | ===== | /
`---' \ ---- A ----- / /
`----'.`-----' /
/ /
'-._ ED /
'. /
`----'
ParmEd: a Parameter file Editor
Loaded Amber topology file com1.prmtop with coordinates from com1.rst7
Reading input from STDIN...
> checkvalidity
Determining validity of prmtop
2 total warnings
MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
Angstroms. Rename CYS to CYX in the PDB file and use the
'bond' command in tleap to create the disulfide bond
LongBondWarning: Atoms 7256 (GLN 449 [C]) and 7258 (ALA 450 [N]) are bonded
(equilibrium length 1.335 A) but are 4.826 A apart. This
often
indicates gaps in the original sequence and should be
checked
carefully.
> printbonds :419,482
Atom 1 Atom 2 R eq Frc Cnst Distance
Energy
6762 N ( N3) 7793 C3 ( c) 1.3790 427.6000 1.3105
2.0071
6759 C ( C) 7786 N1 ( n) 1.3790 427.6000 0.7438
172.5172
6730 CA ( CX) 6728 N ( N) 1.4490 337.0000 1.4343
0.0729
6732 CB ( 3C) 6730 CA ( CX) 1.5260 310.0000 1.5388
0.0510
6734 CG2 ( CT) 6732 CB ( 3C) 1.5260 310.0000 1.5378
0.0430
6738 OG1 ( OH) 6732 CB ( 3C) 1.4100 320.0000 1.4397
0.2817
6740 C ( C) 6730 CA ( CX) 1.5220 317.0000 1.5163
0.0102
6740 C ( C) 6742 N ( N) 1.3350 490.0000 1.3349
0.0000
6741 O ( O) 6740 C ( C) 1.2290 570.0000 1.2507
0.2692
6726 C ( C) 6728 N ( N) 1.3350 490.0000 1.3316
0.0055
7825 C35 ( c3) 7826 C36 ( c) 1.5241 313.0000 1.5720
0.7173
7824 C34 ( c3) 7827 C37 ( c) 1.5241 313.0000 1.5679
0.5996
7823 C33 ( c3) 7825 C35 ( c3) 1.5375 300.9000 1.5527
0.0692
7822 C32 ( c3) 7824 C34 ( c3) 1.5375 300.9000 1.5451
0.0175
7816 C26 ( cf) 7817 C27 ( c2) 1.3461 547.3000 1.3460
0.0000
7814 C24 ( cf) 7815 C25 ( c2) 1.3461 547.3000 1.3487
0.0036
7813 C23 ( cd) 7814 C24 ( cf) 1.4540 386.9000 1.4573
0.0042
7811 C21 ( cd) 7812 C22 ( cf) 1.4540 386.9000 1.3953
1.3345
7811 C21 ( cd) 7813 C23 ( cd) 1.4278 419.8000 1.4569
0.3562
7810 C20 ( cc) 7813 C23 ( cd) 1.3729 500.9000 1.3880
0.1149
7810 C20 ( cc) 7818 C28 ( c3) 1.5015 334.8000 1.4981
0.0039
7809 C19 ( cc) 7810 C20 ( cc) 1.4278 419.8000 1.4439
0.1094
7808 C18 ( cf) 7809 C19 ( cc) 1.3656 513.0000 1.3991
0.5740
7807 C17 ( cf) 7821 C31 ( c3) 1.5157 320.9000 1.5012
0.0678
7806 C16 ( cd) 7807 C17 ( cf) 1.4540 386.9000 1.4492
0.0089
7806 C16 ( cd) 7808 C18 ( cf) 1.4540 386.9000 1.3898
1.5936
7805 C15 ( cc) 7807 C17 ( cf) 1.3656 513.0000 1.3770
0.0663
7805 C15 ( cc) 7822 C32 ( c3) 1.5015 334.8000 1.4993
0.0017
7804 C14 ( cc) 7805 C15 ( cc) 1.4278 419.8000 1.4611
0.4650
7803 C13 ( cf) 7804 C14 ( cc) 1.3656 513.0000 1.3974
0.5184
7802 C12 ( cc) 7820 C30 ( c3) 1.5015 334.8000 1.4989
0.0022
7801 C11 ( cd) 7802 C12 ( cc) 1.3729 500.9000 1.3785
0.0157
7801 C11 ( cd) 7823 C33 ( c3) 1.5015 334.8000 1.5028
0.0005
7800 C10 ( cd) 7801 C11 ( cd) 1.4278 419.8000 1.4618
0.4840
7800 C10 ( cd) 7803 C13 ( cf) 1.4540 386.9000 1.3963
1.2872
7799 C9 ( cc) 7802 C12 ( cc) 1.4278 419.8000 1.4516
0.2383
7798 C8 ( cf) 7799 C9 ( cc) 1.3656 513.0000 1.3929
0.3815
7797 C7 ( cd) 7816 C26 ( cf) 1.4540 386.9000 1.4617
0.0232
7796 C6 ( cc) 7797 C7 ( cd) 1.3729 500.9000 1.3836
0.0573
7796 C6 ( cc) 7819 C29 ( c3) 1.5015 334.8000 1.5002
0.0006
7795 C5 ( cd) 7797 C7 ( cd) 1.4278 419.8000 1.4605
0.4480
7795 C5 ( cd) 7798 C8 ( cf) 1.4540 386.9000 1.3964
1.2825
7794 C4 ( cc) 7796 C6 ( cc) 1.4278 419.8000 1.4447
0.1197
7794 C4 ( cc) 7812 C22 ( cf) 1.3656 513.0000 1.3956
0.4613
7791 C1 ( c3) 7792 C2 ( c3) 1.5375 300.9000 1.5484
0.0355
7791 C1 ( c3) 7793 C3 ( c) 1.5241 313.0000 1.5440
0.1234
7790 N5 ( nc) 7809 C19 ( cc) 1.3694 441.1000 1.3771
0.0262
7790 N5 ( nc) 7811 C21 ( cd) 1.3172 525.4000 1.3725
1.6060
7789 N4 ( nc) 7804 C14 ( cc) 1.3694 441.1000 1.3731
0.0060
7789 N4 ( nc) 7806 C16 ( cd) 1.3172 525.4000 1.3778
1.9298
7788 N3 ( nc) 7799 C9 ( cc) 1.3694 441.1000 1.3768
0.0240
7788 N3 ( nc) 7800 C10 ( cd) 1.3172 525.4000 1.3788
1.9963
7787 N2 ( nc) 7794 C4 ( cc) 1.3694 441.1000 1.3753
0.0155
7787 N2 ( nc) 7795 C5 ( cd) 1.3172 525.4000 1.3700
1.4624
7786 N1 ( n) 7791 C1 ( c3) 1.4619 328.7000 1.4658
0.0050
7785 O5 ( o) 7826 C36 ( c) 1.2183 637.7000 1.2654
1.4139
7784 O4 ( o) 7827 C37 ( c) 1.2183 637.7000 1.2563
0.9220
7783 O3 ( o) 7826 C36 ( c) 1.2183 637.7000 1.2577
0.9917
7782 O2 ( o) 7827 C37 ( c) 1.2183 637.7000 1.2629
1.2704
7781 O1 ( o) 7793 C3 ( c) 1.2183 637.7000 1.2401
0.3039
7780 S1 ( s) 7792 C2 ( c3) 1.8450 212.9000 1.8420
0.0019
7779 Fe1 ( Fe) 7787 N2 ( nc) 2.0000 100.0000 2.2097
4.3971
7779 Fe1 ( Fe) 7790 N5 ( nc) 2.0000 100.0000 2.3362
11.3002
7779 Fe1 ( Fe) 7789 N4 ( nc) 2.0000 100.0000 2.0339
0.1149
7779 Fe1 ( Fe) 7788 N3 ( nc) 2.0000 100.0000 1.8685
1.7287
7779 Fe1 ( Fe) 7780 S1 ( s) 2.6600 80.0000 2.3602
7.1885
6729 H ( H) 6728 N ( N) 1.0100 434.0000 1.0100
0.0000
6731 HA ( H1) 6730 CA ( CX) 1.0900 340.0000 1.0900
0.0000
6733 HB ( H1) 6732 CB ( 3C) 1.0900 340.0000 1.0900
0.0000
6735 HG21 ( HC) 6734 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6736 HG22 ( HC) 6734 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6737 HG23 ( HC) 6734 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6739 HG1 ( HO) 6738 OG1 ( OH) 0.9600 553.0000 0.9600
0.0000
7825 C35 ( c3) 7860 H33 ( hc) 1.0969 330.6000 1.0977
0.0002
7825 C35 ( c3) 7861 H34 ( hc) 1.0969 330.6000 1.0958
0.0004
7824 C34 ( c3) 7858 H31 ( hc) 1.0969 330.6000 1.0988
0.0012
7824 C34 ( c3) 7859 H32 ( hc) 1.0969 330.6000 1.0962
0.0001
7823 C33 ( c3) 7856 H29 ( hc) 1.0969 330.6000 1.0950
0.0012
7823 C33 ( c3) 7857 H30 ( hc) 1.0969 330.6000 1.0987
0.0011
7822 C32 ( c3) 7854 H27 ( hc) 1.0969 330.6000 1.0953
0.0008
7822 C32 ( c3) 7855 H28 ( hc) 1.0969 330.6000 1.0966
0.0000
7821 C31 ( c3) 7851 H24 ( hc) 1.0969 330.6000 1.0977
0.0002
7821 C31 ( c3) 7852 H25 ( hc) 1.0969 330.6000 1.0974
0.0001
7821 C31 ( c3) 7853 H26 ( hc) 1.0969 330.6000 1.0925
0.0064
7820 C30 ( c3) 7848 H21 ( hc) 1.0969 330.6000 1.0969
0.0000
7820 C30 ( c3) 7849 H22 ( hc) 1.0969 330.6000 1.0993
0.0019
7820 C30 ( c3) 7850 H23 ( hc) 1.0969 330.6000 1.0941
0.0025
7819 C29 ( c3) 7845 H18 ( hc) 1.0969 330.6000 1.0931
0.0047
7819 C29 ( c3) 7846 H19 ( hc) 1.0969 330.6000 1.0975
0.0001
7819 C29 ( c3) 7847 H20 ( hc) 1.0969 330.6000 1.0976
0.0001
7818 C28 ( c3) 7842 H15 ( hc) 1.0969 330.6000 1.0945
0.0019
7818 C28 ( c3) 7843 H16 ( hc) 1.0969 330.6000 1.0987
0.0011
7818 C28 ( c3) 7844 H17 ( hc) 1.0969 330.6000 1.0933
0.0043
7817 C27 ( c2) 7840 H13 ( ha) 1.0879 343.1000 1.0848
0.0034
7817 C27 ( c2) 7841 H14 ( ha) 1.0879 343.1000 1.0862
0.0010
7816 C26 ( cf) 7839 H12 ( ha) 1.0883 342.5000 1.0905
0.0016
7815 C25 ( c2) 7837 H10 ( ha) 1.0879 343.1000 1.0853
0.0023
7815 C25 ( c2) 7838 H11 ( ha) 1.0879 343.1000 1.0869
0.0004
7814 C24 ( cf) 7836 H9 ( ha) 1.0883 342.5000 1.0883
0.0000
7812 C22 ( cf) 7835 H8 ( ha) 1.0883 342.5000 1.0839
0.0066
7808 C18 ( cf) 7834 H7 ( ha) 1.0883 342.5000 1.0841
0.0059
7803 C13 ( cf) 7833 H6 ( ha) 1.0883 342.5000 1.0843
0.0056
7798 C8 ( cf) 7832 H5 ( ha) 1.0883 342.5000 1.0832
0.0088
7792 C2 ( c3) 7830 H3 ( h1) 1.0969 330.6000 1.0953
0.0008
7792 C2 ( c3) 7831 H4 ( h1) 1.0969 330.6000 1.0917
0.0091
7791 C1 ( c3) 7829 H2 ( h1) 1.0969 330.6000 1.0925
0.0065
7786 N1 ( n) 7828 H1 ( hn) 1.0129 403.2000 1.0160
0.0039
> printbonds :420,482
Atom 1 Atom 2 R eq Frc Cnst Distance
Energy
6762 N ( N3) 7793 C3 ( c) 1.3790 427.6000 1.3105
2.0071
6744 CA ( CX) 6742 N ( N) 1.4490 337.0000 1.4869
0.4839
6746 CB ( 3C) 6744 CA ( CX) 1.5260 310.0000 1.5402
0.0624
6748 CG2 ( CT) 6746 CB ( 3C) 1.5260 310.0000 1.5186
0.0169
6752 CG1 ( 2C) 6746 CB ( 3C) 1.5260 310.0000 1.5371
0.0382
6755 CD1 ( CT) 6752 CG1 ( 2C) 1.5260 310.0000 1.5089
0.0907
6759 C ( C) 6744 CA ( CX) 1.5220 317.0000 1.5399
0.1016
6759 C ( C) 7786 N1 ( n) 1.3790 427.6000 0.7438
172.5172
6760 O ( O2) 6759 C ( C) 1.2500 656.0000 1.2231
0.4745
6761 OXT ( O2) 6759 C ( C) 1.2500 656.0000 1.2290
0.2893
6740 C ( C) 6742 N ( N) 1.3350 490.0000 1.3349
0.0000
7825 C35 ( c3) 7826 C36 ( c) 1.5241 313.0000 1.5720
0.7173
7824 C34 ( c3) 7827 C37 ( c) 1.5241 313.0000 1.5679
0.5996
7823 C33 ( c3) 7825 C35 ( c3) 1.5375 300.9000 1.5527
0.0692
7822 C32 ( c3) 7824 C34 ( c3) 1.5375 300.9000 1.5451
0.0175
7816 C26 ( cf) 7817 C27 ( c2) 1.3461 547.3000 1.3460
0.0000
7814 C24 ( cf) 7815 C25 ( c2) 1.3461 547.3000 1.3487
0.0036
7813 C23 ( cd) 7814 C24 ( cf) 1.4540 386.9000 1.4573
0.0042
7811 C21 ( cd) 7812 C22 ( cf) 1.4540 386.9000 1.3953
1.3345
7811 C21 ( cd) 7813 C23 ( cd) 1.4278 419.8000 1.4569
0.3562
7810 C20 ( cc) 7813 C23 ( cd) 1.3729 500.9000 1.3880
0.1149
7810 C20 ( cc) 7818 C28 ( c3) 1.5015 334.8000 1.4981
0.0039
7809 C19 ( cc) 7810 C20 ( cc) 1.4278 419.8000 1.4439
0.1094
7808 C18 ( cf) 7809 C19 ( cc) 1.3656 513.0000 1.3991
0.5740
7807 C17 ( cf) 7821 C31 ( c3) 1.5157 320.9000 1.5012
0.0678
7806 C16 ( cd) 7807 C17 ( cf) 1.4540 386.9000 1.4492
0.0089
7806 C16 ( cd) 7808 C18 ( cf) 1.4540 386.9000 1.3898
1.5936
7805 C15 ( cc) 7807 C17 ( cf) 1.3656 513.0000 1.3770
0.0663
7805 C15 ( cc) 7822 C32 ( c3) 1.5015 334.8000 1.4993
0.0017
7804 C14 ( cc) 7805 C15 ( cc) 1.4278 419.8000 1.4611
0.4650
7803 C13 ( cf) 7804 C14 ( cc) 1.3656 513.0000 1.3974
0.5184
7802 C12 ( cc) 7820 C30 ( c3) 1.5015 334.8000 1.4989
0.0022
7801 C11 ( cd) 7802 C12 ( cc) 1.3729 500.9000 1.3785
0.0157
7801 C11 ( cd) 7823 C33 ( c3) 1.5015 334.8000 1.5028
0.0005
7800 C10 ( cd) 7801 C11 ( cd) 1.4278 419.8000 1.4618
0.4840
7800 C10 ( cd) 7803 C13 ( cf) 1.4540 386.9000 1.3963
1.2872
7799 C9 ( cc) 7802 C12 ( cc) 1.4278 419.8000 1.4516
0.2383
7798 C8 ( cf) 7799 C9 ( cc) 1.3656 513.0000 1.3929
0.3815
7797 C7 ( cd) 7816 C26 ( cf) 1.4540 386.9000 1.4617
0.0232
7796 C6 ( cc) 7797 C7 ( cd) 1.3729 500.9000 1.3836
0.0573
7796 C6 ( cc) 7819 C29 ( c3) 1.5015 334.8000 1.5002
0.0006
7795 C5 ( cd) 7797 C7 ( cd) 1.4278 419.8000 1.4605
0.4480
7795 C5 ( cd) 7798 C8 ( cf) 1.4540 386.9000 1.3964
1.2825
7794 C4 ( cc) 7796 C6 ( cc) 1.4278 419.8000 1.4447
0.1197
7794 C4 ( cc) 7812 C22 ( cf) 1.3656 513.0000 1.3956
0.4613
7791 C1 ( c3) 7792 C2 ( c3) 1.5375 300.9000 1.5484
0.0355
7791 C1 ( c3) 7793 C3 ( c) 1.5241 313.0000 1.5440
0.1234
7790 N5 ( nc) 7809 C19 ( cc) 1.3694 441.1000 1.3771
0.0262
7790 N5 ( nc) 7811 C21 ( cd) 1.3172 525.4000 1.3725
1.6060
7789 N4 ( nc) 7804 C14 ( cc) 1.3694 441.1000 1.3731
0.0060
7789 N4 ( nc) 7806 C16 ( cd) 1.3172 525.4000 1.3778
1.9298
7788 N3 ( nc) 7799 C9 ( cc) 1.3694 441.1000 1.3768
0.0240
7788 N3 ( nc) 7800 C10 ( cd) 1.3172 525.4000 1.3788
1.9963
7787 N2 ( nc) 7794 C4 ( cc) 1.3694 441.1000 1.3753
0.0155
7787 N2 ( nc) 7795 C5 ( cd) 1.3172 525.4000 1.3700
1.4624
7786 N1 ( n) 7791 C1 ( c3) 1.4619 328.7000 1.4658
0.0050
7785 O5 ( o) 7826 C36 ( c) 1.2183 637.7000 1.2654
1.4139
7784 O4 ( o) 7827 C37 ( c) 1.2183 637.7000 1.2563
0.9220
7783 O3 ( o) 7826 C36 ( c) 1.2183 637.7000 1.2577
0.9917
7782 O2 ( o) 7827 C37 ( c) 1.2183 637.7000 1.2629
1.2704
7781 O1 ( o) 7793 C3 ( c) 1.2183 637.7000 1.2401
0.3039
7780 S1 ( s) 7792 C2 ( c3) 1.8450 212.9000 1.8420
0.0019
7779 Fe1 ( Fe) 7787 N2 ( nc) 2.0000 100.0000 2.2097
4.3971
7779 Fe1 ( Fe) 7790 N5 ( nc) 2.0000 100.0000 2.3362
11.3002
7779 Fe1 ( Fe) 7789 N4 ( nc) 2.0000 100.0000 2.0339
0.1149
7779 Fe1 ( Fe) 7788 N3 ( nc) 2.0000 100.0000 1.8685
1.7287
7779 Fe1 ( Fe) 7780 S1 ( s) 2.6600 80.0000 2.3602
7.1885
6743 H ( H) 6742 N ( N) 1.0100 434.0000 1.0100
0.0000
6745 HA ( H1) 6744 CA ( CX) 1.0900 340.0000 1.0900
0.0000
6747 HB ( HC) 6746 CB ( 3C) 1.0900 340.0000 1.0900
0.0000
6749 HG21 ( HC) 6748 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6750 HG22 ( HC) 6748 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6751 HG23 ( HC) 6748 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6753 HG12 ( HC) 6752 CG1 ( 2C) 1.0900 340.0000 1.0900
0.0000
6754 HG13 ( HC) 6752 CG1 ( 2C) 1.0900 340.0000 1.0900
0.0000
6756 HD11 ( HC) 6755 CD1 ( CT) 1.0900 340.0000 1.0900
0.0000
6757 HD12 ( HC) 6755 CD1 ( CT) 1.0900 340.0000 1.0900
0.0000
6758 HD13 ( HC) 6755 CD1 ( CT) 1.0900 340.0000 1.0900
0.0000
7825 C35 ( c3) 7860 H33 ( hc) 1.0969 330.6000 1.0977
0.0002
7825 C35 ( c3) 7861 H34 ( hc) 1.0969 330.6000 1.0958
0.0004
7824 C34 ( c3) 7858 H31 ( hc) 1.0969 330.6000 1.0988
0.0012
7824 C34 ( c3) 7859 H32 ( hc) 1.0969 330.6000 1.0962
0.0001
7823 C33 ( c3) 7856 H29 ( hc) 1.0969 330.6000 1.0950
0.0012
7823 C33 ( c3) 7857 H30 ( hc) 1.0969 330.6000 1.0987
0.0011
7822 C32 ( c3) 7854 H27 ( hc) 1.0969 330.6000 1.0953
0.0008
7822 C32 ( c3) 7855 H28 ( hc) 1.0969 330.6000 1.0966
0.0000
7821 C31 ( c3) 7851 H24 ( hc) 1.0969 330.6000 1.0977
0.0002
7821 C31 ( c3) 7852 H25 ( hc) 1.0969 330.6000 1.0974
0.0001
7821 C31 ( c3) 7853 H26 ( hc) 1.0969 330.6000 1.0925
0.0064
7820 C30 ( c3) 7848 H21 ( hc) 1.0969 330.6000 1.0969
0.0000
7820 C30 ( c3) 7849 H22 ( hc) 1.0969 330.6000 1.0993
0.0019
7820 C30 ( c3) 7850 H23 ( hc) 1.0969 330.6000 1.0941
0.0025
7819 C29 ( c3) 7845 H18 ( hc) 1.0969 330.6000 1.0931
0.0047
7819 C29 ( c3) 7846 H19 ( hc) 1.0969 330.6000 1.0975
0.0001
7819 C29 ( c3) 7847 H20 ( hc) 1.0969 330.6000 1.0976
0.0001
7818 C28 ( c3) 7842 H15 ( hc) 1.0969 330.6000 1.0945
0.0019
7818 C28 ( c3) 7843 H16 ( hc) 1.0969 330.6000 1.0987
0.0011
7818 C28 ( c3) 7844 H17 ( hc) 1.0969 330.6000 1.0933
0.0043
7817 C27 ( c2) 7840 H13 ( ha) 1.0879 343.1000 1.0848
0.0034
7817 C27 ( c2) 7841 H14 ( ha) 1.0879 343.1000 1.0862
0.0010
7816 C26 ( cf) 7839 H12 ( ha) 1.0883 342.5000 1.0905
0.0016
7815 C25 ( c2) 7837 H10 ( ha) 1.0879 343.1000 1.0853
0.0023
7815 C25 ( c2) 7838 H11 ( ha) 1.0879 343.1000 1.0869
0.0004
7814 C24 ( cf) 7836 H9 ( ha) 1.0883 342.5000 1.0883
0.0000
7812 C22 ( cf) 7835 H8 ( ha) 1.0883 342.5000 1.0839
0.0066
7808 C18 ( cf) 7834 H7 ( ha) 1.0883 342.5000 1.0841
0.0059
7803 C13 ( cf) 7833 H6 ( ha) 1.0883 342.5000 1.0843
0.0056
7798 C8 ( cf) 7832 H5 ( ha) 1.0883 342.5000 1.0832
0.0088
7792 C2 ( c3) 7830 H3 ( h1) 1.0969 330.6000 1.0953
0.0008
7792 C2 ( c3) 7831 H4 ( h1) 1.0969 330.6000 1.0917
0.0091
7791 C1 ( c3) 7829 H2 ( h1) 1.0969 330.6000 1.0925
0.0065
7786 N1 ( n) 7828 H1 ( hn) 1.0129 403.2000 1.0160
0.0039
>
(base) [exx.c107739 xleap-mol2]$ tleap
-I: Adding /usr/local/amber18/dat/leap/prep to search path.
-I: Adding /usr/local/amber18/dat/leap/lib to search path.
-I: Adding /usr/local/amber18/dat/leap/parm to search path.
-I: Adding /usr/local/amber18/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.protein.ff14SB
----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/local/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/local/amber18/dat/leap/lib/amino12.lib
Loading library: /usr/local/amber18/dat/leap/lib/aminoct12.lib
Loading library: /usr/local/amber18/dat/leap/lib/aminont12.lib
> source leaprc.gaff
----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
> loadamberparams test-uncap1.frcmod
Loading parameters: ./test-uncap1.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> HEM = loadmol2 test-uncap3.mol2
Loading Mol2 file: ./test-uncap3.mol2
Reading MOLECULE named HEM
> 3v8d = loadpdb 3v8d-prep.pdb
Loading PDB file: ./3v8d-prep.pdb
Added missing heavy atom: .R<NSER 1>.A<OG 10>
Added missing heavy atom: .R<ARG 3>.A<CG 8>
Added missing heavy atom: .R<ARG 3>.A<CD 11>
Added missing heavy atom: .R<ARG 3>.A<NE 14>
Added missing heavy atom: .R<ARG 3>.A<CZ 16>
Added missing heavy atom: .R<ARG 3>.A<NH1 17>
Added missing heavy atom: .R<ARG 3>.A<NH2 20>
Added missing heavy atom: .R<ASN 13>.A<CG 8>
Added missing heavy atom: .R<ASN 13>.A<OD1 9>
Added missing heavy atom: .R<ASN 13>.A<ND2 10>
Added missing heavy atom: .R<LYS 39>.A<CE 14>
Added missing heavy atom: .R<LYS 39>.A<NZ 17>
Added missing heavy atom: .R<LYS 64>.A<NZ 17>
Added missing heavy atom: .R<LYS 70>.A<CG 8>
Added missing heavy atom: .R<LYS 70>.A<CD 11>
Added missing heavy atom: .R<LYS 70>.A<CE 14>
Added missing heavy atom: .R<LYS 70>.A<NZ 17>
Added missing heavy atom: .R<MET 94>.A<CG 8>
Added missing heavy atom: .R<MET 94>.A<SD 11>
Added missing heavy atom: .R<MET 94>.A<CE 12>
Added missing heavy atom: .R<LYS 108>.A<CD 11>
Added missing heavy atom: .R<LYS 108>.A<CE 14>
Added missing heavy atom: .R<LYS 108>.A<NZ 17>
Added missing heavy atom: .R<GLU 120>.A<CD 11>
Added missing heavy atom: .R<GLU 120>.A<OE1 12>
Added missing heavy atom: .R<GLU 120>.A<OE2 13>
Added missing heavy atom: .R<SER 135>.A<OG 8>
Added missing heavy atom: .R<LYS 139>.A<CG 8>
Added missing heavy atom: .R<LYS 139>.A<CD 11>
Added missing heavy atom: .R<LYS 139>.A<CE 14>
Added missing heavy atom: .R<LYS 139>.A<NZ 17>
Added missing heavy atom: .R<LYS 176>.A<CD 11>
Added missing heavy atom: .R<LYS 176>.A<CE 14>
Added missing heavy atom: .R<LYS 176>.A<NZ 17>
Added missing heavy atom: .R<ARG 206>.A<NE 14>
Added missing heavy atom: .R<ARG 206>.A<CZ 16>
Added missing heavy atom: .R<ARG 206>.A<NH1 17>
Added missing heavy atom: .R<ARG 206>.A<NH2 20>
Added missing heavy atom: .R<GLU 222>.A<CG 8>
Added missing heavy atom: .R<GLU 222>.A<CD 11>
Added missing heavy atom: .R<GLU 222>.A<OE1 12>
Added missing heavy atom: .R<GLU 222>.A<OE2 13>
Added missing heavy atom: .R<LYS 226>.A<CE 14>
Added missing heavy atom: .R<LYS 226>.A<NZ 17>
Added missing heavy atom: .R<GLU 283>.A<CD 11>
Added missing heavy atom: .R<GLU 283>.A<OE1 12>
Added missing heavy atom: .R<GLU 283>.A<OE2 13>
Added missing heavy atom: .R<LYS 286>.A<CE 14>
Added missing heavy atom: .R<LYS 286>.A<NZ 17>
Added missing heavy atom: .R<LYS 302>.A<CG 8>
Added missing heavy atom: .R<LYS 302>.A<CD 11>
Added missing heavy atom: .R<LYS 302>.A<CE 14>
Added missing heavy atom: .R<LYS 302>.A<NZ 17>
Added missing heavy atom: .R<GLU 306>.A<CG 8>
Added missing heavy atom: .R<GLU 306>.A<CD 11>
Added missing heavy atom: .R<GLU 306>.A<OE1 12>
Added missing heavy atom: .R<GLU 306>.A<OE2 13>
Added missing heavy atom: .R<ASN 308>.A<CG 8>
Added missing heavy atom: .R<ASN 308>.A<OD1 9>
Added missing heavy atom: .R<ASN 308>.A<ND2 10>
Added missing heavy atom: .R<GLU 392>.A<CG 8>
Added missing heavy atom: .R<GLU 392>.A<CD 11>
Added missing heavy atom: .R<GLU 392>.A<OE1 12>
Added missing heavy atom: .R<GLU 392>.A<OE2 13>
Added missing heavy atom: .R<LYS 395>.A<CG 8>
Added missing heavy atom: .R<LYS 395>.A<CD 11>
Added missing heavy atom: .R<LYS 395>.A<CE 14>
Added missing heavy atom: .R<LYS 395>.A<NZ 17>
Added missing heavy atom: .R<CILE 420>.A<OXT 20>
Added missing heavy atom: .R<GLU 442>.A<OE1 12>
Added missing heavy atom: .R<GLU 442>.A<OE2 13>
Added missing heavy atom: .R<LYS 451>.A<CG 8>
Added missing heavy atom: .R<LYS 451>.A<CD 11>
Added missing heavy atom: .R<LYS 451>.A<CE 14>
Added missing heavy atom: .R<LYS 451>.A<NZ 17>
Added missing heavy atom: .R<CHIE 481>.A<OXT 18>
Added missing heavy atom: .R<CHIE 481>.A<CG 8>
Added missing heavy atom: .R<CHIE 481>.A<ND1 9>
Added missing heavy atom: .R<CHIE 481>.A<CD2 14>
Added missing heavy atom: .R<CHIE 481>.A<CE1 10>
Added missing heavy atom: .R<CHIE 481>.A<NE2 12>
total atoms in file: 3813
Leap added 3965 missing atoms according to residue templates:
81 Heavy
3884 H / lone pairs
> com = combine { 3v8d HEM }
> bond com.482.C3 com.421.N
> bond com.420.C com.482.N1
> saveamberparm com com1.prmtop com1.rst7
Checking Unit.
Warning: There is a bond of 4.825647 angstroms between:
Warning: The unperturbed charge of the unit (3.077800) is not integral.
Warning: The unperturbed charge of the unit (3.077800) is not zero.
Note: Ignoring the error and warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1612 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CHIE 1
CILE 1
HEM 1
NPRO 1
NSER 1
)
(no restraints)
> quit
Quit
On Tue, Feb 18, 2020 at 1:02 AM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Feb 17, 2020, Vaibhav Dixit wrote:
>
> >As suggested by David, I tried parmed on prmtop/rst7 files.
>
> Sorry: I wasn't more specific: in addition to "checkvalidity", use the
> printBonds commands to see all the bonds in some mask.
>
> Here are the bonds that you asked tleap to add:
>
> >bond com.482.C3 com.420.N
> >bond com.419.C com.482.N1
>
> So, in parmed, you can type "printbonds ':419,420,482'" to see if they
> are indeed there.
>
> Note also that the numbering scheme used here is the internal Amber
> scheme, so make sure that residue 482 (etc.) is indeed the residue you
> intended.
>
> ...hope this helps....dac
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Mon Feb 17 2020 - 20:00:02 PST
