[gmx-users] long-bond warning during running
nitu sharma
sharmanitu35 at gmail.com
Fri Jul 3 15:24:12 CEST 2009
Dear all
I am doing simulation of Dna-protein complex with using amber tools
with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have made lot of
changes in .pdb file after that "pdb2gmx " starts working but it give to
many warnings. like-
Warning: Long Bond (291-293 = 0.86645 nm)
Warning: Long Bond (291-310 = 1.08462 nm)
Warning: Long Bond (293-294 = 0.429679 nm)
Warning: Long Bond (293-307 = 0.767604 nm)
Warning: Long Bond (294-296 = 0.443442 nm)
Warning: Long Bond (297-298 = 0.737835 nm)
Warning: Long Bond (297-307 = 0.595315 nm)
Warning: Long Bond (298-299 = 0.808366 nm)
Warning: Long Bond (298-300 = 0.707622 nm)
Warning: Long Bond (300-302 = 0.738664 nm)
Warning: Long Bond (302-303 = 0.860242 nm)
Warning: Long Bond (302-306 = 0.427252 nm)
Warning: Long Bond (306-307 = 0.60875 nm)
Warning: Long Bond (308-310 = 0.931786 nm)
Warning: Long Bond (308-313 = 0.828688 nm)
Warning: Long Bond (280-281 = 0.417096 nm)
Warning: Long Bond (314-315 = 0.265962 nm)
Warning: Long Bond (314-316 = 0.501846 nm)
Warning: Long Bond (314-317 = 0.407156 nm)
Warning: Long Bond (317-318 = 0.316267 nm)
Warning: Long Bond (321-323 = 0.735348 nm)
Warning: Long Bond (321-336 = 0.672012 nm)
Warning: Long Bond (323-324 = 0.634508 nm)
Warning: Long Bond (326-327 = 0.510123 nm)
Warning: Long Bond (326-334 = 0.951643 nm)
Warning: Long Bond (327-329 = 0.510298 nm)
Warning: Long Bond (329-330 = 0.433539 nm)
Warning: Long Bond (330-331 = 0.458922 nm)
Warning: Long Bond (332-334 = 0.592297 nm)
Warning: Long Bond (334-335 = 0.412661 nm)
Warning: Long Bond (336-338 = 0.907703 nm)
Warning: Long Bond (336-341 = 0.905717 nm)
Warning: Long Bond (313-314 = 0.702567 nm)
Warning: Long Bond (342-343 = 0.704904 nm)
Warning: Long Bond (342-344 = 0.808923 nm)
Warning: Long Bond (342-345 = 0.860233 nm)
Warning: Long Bond (349-369 = 0.402523 nm)
Warning: Long Bond (351-352 = 0.825131 nm)
Warning: Long Bond (352-354 = 0.708667 nm)
Warning: Long Bond (352-371 = 0.772094 nm)
Warning: Long Bond (354-355 = 0.431195 nm)
Warning: Long Bond (354-368 = 0.342288 nm)
Warning: Long Bond (355-357 = 0.514821 nm)
Warning: Long Bond (357-358 = 0.517131 nm)
Warning: Long Bond (359-360 = 0.640538 nm)
Warning: Long Bond (359-361 = 0.511957 nm)
Warning: Long Bond (361-363 = 0.632475 nm)
Warning: Long Bond (363-364 = 0.252832 nm)
Warning: Long Bond (363-367 = 0.550244 nm)
Warning: Long Bond (367-368 = 0.593196 nm)
Warning: Long Bond (369-371 = 0.415453 nm)
Warning: Long Bond (369-374 = 0.611634 nm)
Warning: Long Bond (341-342 = 0.830307 nm)
Warning: Long Bond (375-378 = 0.422488 nm)
Warning: Long Bond (378-379 = 0.251446 nm)
Warning: Short Bond (382-384 = 0.034 nm)
Warning: Long Bond (382-397 = 0.360644 nm)
Warning: Long Bond (384-385 = 0.448028 nm)
Warning: Long Bond (385-387 = 0.854859 nm)
Warning: Long Bond (385-399 = 0.898552 nm)
Warning: Long Bond (387-388 = 0.341151 nm)
Warning: Long Bond (387-395 = 0.64161 nm)
Warning: Long Bond (388-390 = 0.583816 nm)
Warning: Long Bond (390-391 = 0.460305 nm)
Warning: Long Bond (391-393 = 0.596343 nm)
Warning: Long Bond (393-395 = 0.510843 nm)
Warning: Long Bond (395-396 = 0.378148 nm)
Warning: Long Bond (397-399 = 0.922111 nm)
Warning: Long Bond (397-402 = 0.596553 nm)
Warning: Long Bond (374-375 = 0.40299 nm)
Warning: Long Bond (403-404 = 0.637247 nm)
Warning: Long Bond (404-407 = 0.318624 nm)
Warning: Long Bond (407-409 = 0.379685 nm)
Warning: Long Bond (407-426 = 0.543994 nm)
Warning: Long Bond (409-410 = 0.500324 nm)
Warning: Long Bond (410-428 = 0.609291 nm)
Warning: Long Bond (412-425 = 0.788185 nm)
Warning: Long Bond (413-415 = 0.791283 nm)
Warning: Long Bond (415-416 = 0.708127 nm)
Warning: Long Bond (416-417 = 0.255204 nm)
Warning: Long Bond (416-425 = 0.715307 nm)
Warning: Long Bond (417-418 = 0.618501 nm)
Warning: Long Bond (417-421 = 0.670827 nm)
Warning: Long Bond (421-422 = 0.950023 nm)
Warning: Long Bond (422-424 = 0.717385 nm)
Warning: Long Bond (424-425 = 1.08167 nm)
Warning: Long Bond (426-428 = 0.511531 nm)
Warning: Long Bond (426-431 = 1.08592 nm)
Warning: Long Bond (432-433 = 0.912686 nm)
Warning: Long Bond (432-435 = 0.519809 nm)
Warning: Long Bond (435-436 = 0.450706 nm)
Warning: Long Bond (436-439 = 0.325467 nm)
Warning: Long Bond (439-441 = 0.719692 nm)
Warning: Long Bond (439-456 = 0.856575 nm)
Warning: Long Bond (441-442 = 0.700777 nm)
Warning: Long Bond (442-444 = 0.617616 nm)
Warning: Long Bond (442-458 = 0.526962 nm)
Warning: Long Bond (444-445 = 0.608832 nm)
Warning: Long Bond (444-454 = 0.466287 nm)
Warning: Long Bond (447-449 = 0.719506 nm)
Warning: Long Bond (449-453 = 0.400781 nm)
Warning: Long Bond (454-455 = 0.781281 nm)
Warning: Long Bond (456-458 = 0.43477 nm)
Warning: Long Bond (456-461 = 0.854421 nm)
Warning: Long Bond (431-432 = 1.14334 nm)
Warning: Long Bond (462-463 = 0.675814 nm)
Warning: Long Bond (462-464 = 0.429367 nm)
Warning: Long Bond (462-465 = 0.92747 nm)
Warning: Long Bond (465-466 = 0.61628 nm)
Warning: Long Bond (466-469 = 0.813831 nm)
Warning: Long Bond (469-471 = 0.829303 nm)
Warning: Long Bond (471-472 = 1.0632 nm)
Warning: Long Bond (472-474 = 0.990568 nm)
Warning: Long Bond (472-490 = 0.419376 nm)
Warning: Long Bond (474-475 = 0.864227 nm)
Warning: Long Bond (474-487 = 0.382602 nm)
Warning: Long Bond (475-477 = 0.851014 nm)
Warning: Long Bond (477-478 = 0.683878 nm)
Warning: Long Bond (478-479 = 0.68112 nm)
Warning: Long Bond (478-487 = 0.707226 nm)
Warning: Long Bond (479-480 = 0.608289 nm)
Warning: Long Bond (479-483 = 0.619426 nm)
Warning: Long Bond (483-484 = 0.608289 nm)
Warning: Long Bond (486-487 = 0.72991 nm)
Warning: Long Bond (488-490 = 0.500783 nm)
Warning: Long Bond (488-493 = 0.852481 nm)
Warning: Long Bond (461-462 = 0.80635 nm)
Warning: Long Bond (494-495 = 0.509133 nm)
Warning: Long Bond (494-496 = 0.836758 nm)
Warning: Long Bond (494-497 = 0.316253 nm)
Warning: Long Bond (497-498 = 0.728011 nm)
Warning: Long Bond (501-503 = 0.5657 nm)
Warning: Long Bond (501-518 = 0.813968 nm)
Warning: Long Bond (503-504 = 0.252367 nm)
Warning: Long Bond (504-506 = 0.608967 nm)
Warning: Short Bond (504-520 = 0.038 nm)
Warning: Long Bond (506-507 = 0.644884 nm)
Warning: Long Bond (506-516 = 0.860828 nm)
Warning: Long Bond (507-509 = 0.413068 nm)
Warning: Long Bond (509-511 = 0.376962 nm)
Warning: Long Bond (511-512 = 0.361055 nm)
Warning: Long Bond (511-515 = 0.652019 nm)
Warning: Long Bond (515-516 = 1.1316 nm)
Warning: Long Bond (516-517 = 0.912686 nm)
Warning: Long Bond (518-523 = 0.769769 nm)
Warning: Long Bond (493-494 = 0.901619 nm)
Warning: Long Bond (524-525 = 0.945918 nm)
Warning: Long Bond (524-527 = 0.334162 nm)
Warning: Long Bond (527-528 = 0.92624 nm)
Warning: Long Bond (531-533 = 0.674158 nm)
Warning: Long Bond (531-546 = 0.322639 nm)
Warning: Long Bond (533-534 = 0.905884 nm)
Warning: Long Bond (534-536 = 0.709384 nm)
Warning: Long Bond (534-548 = 0.448357 nm)
Warning: Long Bond (536-537 = 0.644884 nm)
Warning: Long Bond (536-544 = 0.721416 nm)
Warning: Long Bond (539-540 = 0.943517 nm)
Warning: Long Bond (540-541 = 1.14404 nm)
Warning: Long Bond (540-542 = 0.957414 nm)
Warning: Long Bond (542-544 = 0.415655 nm)
Warning: Long Bond (544-545 = 0.549837 nm)
Warning: Long Bond (546-548 = 0.731762 nm)
Warning: Long Bond (546-551 = 0.87139 nm)
Warning: Long Bond (523-524 = 0.81204 nm)
Warning: Long Bond (552-553 = 0.614348 nm)
Warning: Long Bond (552-554 = 0.321685 nm)
Warning: Long Bond (552-555 = 0.721166 nm)
Warning: Long Bond (555-556 = 0.825959 nm)
Warning: Long Bond (556-559 = 0.282929 nm)
Warning: Long Bond (559-561 = 0.383275 nm)
Warning: Long Bond (559-574 = 0.362062 nm)
Warning: Long Bond (561-562 = 0.700874 nm)
Warning: Long Bond (562-576 = 0.611955 nm)
Warning: Long Bond (564-565 = 0.453625 nm)
Warning: Long Bond (564-572 = 0.32187 nm)
Warning: Long Bond (565-567 = 0.614781 nm)
Warning: Long Bond (567-568 = 0.924608 nm)
Warning: Long Bond (568-569 = 0.863067 nm)
Warning: Long Bond (568-570 = 0.810385 nm)
Warning: Long Bond (570-572 = 0.582275 nm)
Warning: Long Bond (572-573 = 0.709908 nm)
Warning: Long Bond (574-576 = 0.732913 nm)
Warning: Long Bond (574-579 = 0.331662 nm)
Warning: Long Bond (551-552 = 0.911265 nm)
Warning: Long Bond (580-581 = 0.9597 nm)
Warning: Long Bond (580-582 = 0.722773 nm)
Warning: Long Bond (580-583 = 0.7294 nm)
Warning: Long Bond (583-584 = 0.442579 nm)
Warning: Long Bond (584-587 = 0.360605 nm)
Warning: Long Bond (587-589 = 0.719506 nm)
Warning: Long Bond (587-604 = 0.583288 nm)
Warning: Long Bond (589-590 = 0.852015 nm)
Warning: Long Bond (590-592 = 0.516124 nm)
Warning: Long Bond (592-593 = 0.761609 nm)
Warning: Long Bond (595-597 = 0.929223 nm)
Warning: Long Bond (597-598 = 0.815255 nm)
Warning: Short Bond (597-601 = 0.00600001 nm)
Warning: Long Bond (601-602 = 0.379685 nm)
Warning: Long Bond (602-603 = 0.5001 nm)
Warning: Long Bond (604-606 = 0.520047 nm)
Warning: Long Bond (604-609 = 0.764519 nm)
Warning: Long Bond (579-580 = 0.828788 nm)
Warning: Long Bond (610-611 = 0.435211 nm)
Warning: Long Bond (610-613 = 0.720833 nm)
Warning: Long Bond (613-614 = 0.612406 nm)
Warning: Long Bond (614-617 = 0.598071 nm)
Warning: Long Bond (617-619 = 0.728288 nm)
Warning: Long Bond (617-634 = 0.948709 nm)
Warning: Long Bond (620-636 = 0.830906 nm)
Warning: Long Bond (622-623 = 0.322639 nm)
Warning: Long Bond (622-632 = 0.683492 nm)
Warning: Long Bond (623-625 = 0.907659 nm)
Warning: Long Bond (625-627 = 0.433849 nm)
Warning: Long Bond (627-631 = 0.503829 nm)
Warning: Long Bond (631-632 = 0.366191 nm)
Warning: Long Bond (634-636 = 0.645046 nm)
Warning: Long Bond (634-639 = 0.405408 nm)
Warning: Long Bond (609-610 = 0.31805 nm)
Warning: Long Bond (640-641 = 0.949004 nm)
Warning: Long Bond (640-642 = 0.302655 nm)
Warning: Long Bond (643-644 = 0.7245 nm)
Warning: Long Bond (644-647 = 0.722225 nm)
Warning: Long Bond (647-649 = 0.808923 nm)
Warning: Long Bond (647-667 = 0.361565 nm)
Warning: Long Bond (649-650 = 0.710563 nm)
Warning: Long Bond (650-652 = 1.14018 nm)
Warning: Long Bond (650-669 = 0.367098 nm)
Warning: Long Bond (652-653 = 0.990257 nm)
Warning: Long Bond (652-666 = 0.458477 nm)
Warning: Long Bond (653-655 = 0.707661 nm)
Warning: Long Bond (655-656 = 0.525967 nm)
Warning: Long Bond (656-657 = 0.544875 nm)
Warning: Long Bond (656-666 = 0.414981 nm)
Warning: Long Bond (657-658 = 0.500529 nm)
Warning: Long Bond (661-662 = 0.514669 nm)
Warning: Long Bond (661-665 = 0.431017 nm)
Warning: Long Bond (665-666 = 0.462775 nm)
Warning: Long Bond (667-669 = 0.501597 nm)
Warning: Long Bond (673-674 = 0.361641 nm)
Warning: Long Bond (673-675 = 0.508759 nm)
Warning: Long Bond (673-676 = 0.836254 nm)
Warning: Long Bond (676-677 = 0.331362 nm)
Warning: Long Bond (677-680 = 0.737835 nm)
Warning: Long Bond (680-682 = 1.14054 nm)
Warning: Long Bond (680-700 = 0.922697 nm)
Warning: Long Bond (682-683 = 0.501597 nm)
Warning: Long Bond (683-685 = 0.506679 nm)
Warning: Long Bond (683-702 = 0.761725 nm)
Warning: Long Bond (685-686 = 0.957961 nm)
Warning: Long Bond (686-688 = 0.861357 nm)
Warning: Long Bond (688-689 = 0.460783 nm)
Warning: Long Bond (689-690 = 0.424566 nm)
Warning: Long Bond (690-691 = 0.4325 nm)
Warning: Long Bond (690-692 = 0.553986 nm)
Warning: Long Bond (692-694 = 0.812779 nm)
Warning: Long Bond (694-695 = 0.681469 nm)
Warning: Long Bond (694-698 = 0.806331 nm)
Warning: Long Bond (700-702 = 0.895366 nm)
Warning: Long Bond (700-705 = 0.346238 nm)
Warning: Long Bond (672-673 = 0.44989 nm)
Warning: Long Bond (706-707 = 0.328513 nm)
Warning: Long Bond (709-710 = 0.711179 nm)
Warning: Long Bond (710-713 = 0.638548 nm)
Warning: Long Bond (713-715 = 0.45449 nm)
Warning: Long Bond (713-728 = 0.543177 nm)
Warning: Long Bond (715-716 = 0.728187 nm)
Warning: Long Bond (716-718 = 0.553986 nm)
Warning: Long Bond (716-730 = 0.826259 nm)
Warning: Long Bond (718-719 = 0.512173 nm)
Warning: Long Bond (718-726 = 0.707141 nm)
Warning: Long Bond (719-721 = 0.578692 nm)
Warning: Long Bond (721-722 = 0.316583 nm)
Warning: Long Bond (722-723 = 0.413807 nm)
Warning: Long Bond (722-724 = 0.912938 nm)
Warning: Long Bond (724-726 = 0.325 nm)
Warning: Long Bond (726-727 = 0.910719 nm)
Warning: Long Bond (728-730 = 0.864324 nm)
Warning: Long Bond (728-733 = 0.719322 nm)
Warning: Long Bond (734-735 = 0.835924 nm)
Warning: Long Bond (734-736 = 0.503353 nm)
Warning: Long Bond (734-737 = 0.51 nm)
Warning: Long Bond (737-738 = 0.361288 nm)
Warning: Long Bond (738-741 = 0.608297 nm)
Warning: Long Bond (741-743 = 1.13952 nm)
Warning: Long Bond (741-758 = 0.406079 nm)
Warning: Long Bond (743-744 = 0.608639 nm)
Warning: Long Bond (744-746 = 0.646913 nm)
Warning: Long Bond (744-760 = 0.729756 nm)
Warning: Long Bond (746-747 = 0.632911 nm)
Warning: Long Bond (746-756 = 0.33289 nm)
Warning: Long Bond (747-749 = 0.612679 nm)
Warning: Long Bond (749-751 = 0.860828 nm)
Warning: Long Bond (751-752 = 0.644885 nm)
Warning: Long Bond (751-755 = 0.566153 nm)
Warning: Long Bond (755-756 = 0.431133 nm)
Warning: Long Bond (756-757 = 0.413068 nm)
Warning: Long Bond (758-760 = 0.619052 nm)
Warning: Long Bond (733-734 = 0.61628 nm)
Warning: Long Bond (764-765 = 0.732735 nm)
Warning: Long Bond (764-767 = 0.322248 nm)
Warning: Long Bond (767-768 = 0.501597 nm)
Warning: Long Bond (768-771 = 0.327194 nm)
Warning: Long Bond (771-773 = 0.653979 nm)
Warning: Long Bond (771-790 = 0.450706 nm)
Warning: Long Bond (773-774 = 0.608875 nm)
Warning: Long Bond (774-792 = 0.434161 nm)
Warning: Long Bond (776-777 = 0.633537 nm)
Warning: Long Bond (776-789 = 0.793123 nm)
Warning: Long Bond (777-779 = 0.519809 nm)
Warning: Long Bond (779-780 = 0.789015 nm)
Warning: Long Bond (780-781 = 0.720447 nm)
Warning: Long Bond (781-782 = 0.540926 nm)
Warning: Long Bond (781-785 = 0.676184 nm)
Warning: Long Bond (785-786 = 0.63459 nm)
Warning: Long Bond (786-788 = 0.613294 nm)
Warning: Long Bond (788-789 = 0.420386 nm)
Warning: Long Bond (790-792 = 0.50636 nm)
Warning: Long Bond (763-764 = 0.374979 nm)
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: atom P is missing in residue DT 1 in the pdb file
WARNING: atom O1P is missing in residue DT 1 in the pdb file
WARNING: atom O2P is missing in residue DT 1 in the pdb file
WARNING: atom C7 is missing in residue DT 1 in the pdb file
WARNING: atom H71 is missing in residue DT 1 in the pdb file
You might need to add atom H71 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H72 is missing in residue DT 1 in the pdb file
You might need to add atom H72 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H73 is missing in residue DT 1 in the pdb file
You might need to add atom H73 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom C7 is missing in residue DT 11 in the pdb file
WARNING: atom H71 is missing in residue DT 11 in the pdb file
You might need to add atom H71 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H72 is missing in residue DT 11 in the pdb file
You might need to add atom H72 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H73 is missing in residue DT 11 in the pdb file
You might need to add atom H73 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom C7 is missing in residue DT 13 in the pdb file
WARNING: atom H71 is missing in residue DT 13 in the pdb file
You might need to add atom H71 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H72 is missing in residue DT 13 in the pdb file
You might need to add atom H72 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H73 is missing in residue DT 13 in the pdb file
You might need to add atom H73 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom P is missing in residue DA 14 in the pdb file
WARNING: atom O1P is missing in residue DA 14 in the pdb file
WARNING: atom O2P is missing in residue DA 14 in the pdb file
WARNING: atom C7 is missing in residue DT 18 in the pdb file
WARNING: atom H71 is missing in residue DT 18 in the pdb file
You might need to add atom H71 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H72 is missing in residue DT 18 in the pdb file
You might need to add atom H72 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H73 is missing in residue DT 18 in the pdb file
You might need to add atom H73 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom C7 is missing in residue DT 19 in the pdb file
WARNING: atom H71 is missing in residue DT 19 in the pdb file
You might need to add atom H71 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H72 is missing in residue DT 19 in the pdb file
You might need to add atom H72 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H73 is missing in residue DT 19 in the pdb file
You might need to add atom H73 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom C7 is missing in residue DT 24 in the pdb file
WARNING: atom H71 is missing in residue DT 24 in the pdb file
You might need to add atom H71 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H72 is missing in residue DT 24 in the pdb file
You might need to add atom H72 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
WARNING: atom H73 is missing in residue DT 24 in the pdb file
You might need to add atom H73 to the hydrogen database of residue
DT
in the file ff???.hdb (see the manual)
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.3
Source code file: pdb2top.c, line: 704
Fatal error:
There were 30 missing atoms in molecule Protein_A, if you want to use this
incomplete topology anyhow, use the option -missing
-------------------------------------------------------
"Does All This Money Really Have To Go To Charity ?" (Rick
so if anyone have idea about this please suggest me can I use missing
option for further processing .
or If it will make harm to simulation process please suggest me something to
solve this long bond problem.
Thanking you
Nitu sharma.
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