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Dear Amber community,
I am preparing a large molecule (~1100 atoms) for simulation in sander,
using amber7. It went fine through antechamber giving me a prepin file.
For some reason, don't know why, parmchk crashes (parmchk -i file.prepin
-f prepi -o frcmod).
Reading it into xleap nonetheless, when doing (after loading leaprc.gaff,
and loadamberprep)
saveamberparm UNK prmtop prmcrd
it gives me several warnings of this nature:
WARNING: There is a bond of 125.626000 angstroms between:
----------- .R<UNK 1>.A<N70 998> and .R<UNK 1>.A<C17 999>
It then ignores these warnings and builds the topology, atom, bond etc.
parameters.
My question is, are warnings like these commonly seen? Do I have to be
worried about them, and what do I have to do about them to make them
dissapear? Below I will attach some of the lines of the pdb and prepin file.
Thanks,
Armin
pdb
ATOM 300 H165UNK 1 14.367 -7.635 -2.980 1.00 0.00
ATOM 301 N35 UNK 1 11.647 -6.613 -0.495 1.00 0.00
ATOM 302 H166UNK 1 10.757 -6.425 -0.939 1.00 0.00
ATOM 303 H167UNK 1 11.540 -7.177 0.367 1.00 0.00
ATOM 304 C83 UNK 1 14.136 -6.476 -4.705 1.00 0.00
ATOM 305 O17 UNK 1 13.271 -5.890 -5.308 1.00 0.00
ATOM 306 C84 UNK 1 15.180 -8.007 -6.508 1.00 0.00
ATOM 307 H168UNK 1 14.964 -8.882 -5.892 1.00 0.00
ATOM 308 H169UNK 1 16.011 -8.246 -7.217 1.00 0.00
ATOM 309 C85 UNK 1 15.477 -6.895 -5.460 1.00 0.00
ATOM 310 H170UNK 1 15.791 -6.035 -6.161 1.00 0.00
ATOM 311 H171UNK 1 16.318 -6.979 -4.757 1.00 0.00
ATOM 312 N36 UNK 1 13.916 -7.777 -7.308 1.00 0.00
ATOM 313 C86 UNK 1 12.933 -9.621 -8.695 1.00 0.00
ATOM 314 H172UNK 1 12.710 -8.929 -9.535 1.00 0.00
ATOM 315 H173UNK 1 12.108 -10.343 -8.522 1.00 0.00
ATOM 316 C87 UNK 1 12.912 -8.786 -7.423 1.00 0.00
ATOM 317 H174UNK 1 12.966 -9.508 -6.644 1.00 0.00
ATOM 318 H175UNK 1 11.951 -8.319 -7.394 1.00 0.00
ATOM 319 C88 UNK 1 14.216 -10.461 -8.924 1.00 0.00
ATOM 320 O18 UNK 1 15.047 -10.630 -8.031 1.00 0.00
prepin
300 H15 hc E 298 297 296 1.135 108.545 -53.114 0.000
301 C80 c B 298 297 296 1.552 110.831 -169.304 0.000
302 O16 o E 301 298 297 1.246 120.160 -97.203 0.000
303 N39 n B 301 298 297 1.334 120.293 88.100 0.000
304 C92 c3 3 303 301 298 1.495 127.495 -8.489 0.000
305 C91 c3 3 304 303 301 1.551 107.857 -166.803 0.000
306 N36 n3 B 305 304 303 1.507 113.972 172.631 0.000
307 C84 c3 3 306 305 304 1.513 116.980 -153.121 0.000
308 H16 h1 E 307 306 305 1.092 104.763 -166.531 0.000
309 H16 h1 E 307 306 305 1.118 108.541 -49.649 0.000
310 C85 c3 3 307 306 305 1.557 113.995 81.250 0.000
311 C83 c B 310 307 306 1.595 110.240 42.440 0.000
312 N34 n B 311 310 307 1.377 122.706 103.065 0.000
313 C81 c3 3 312 311 310 1.409 120.918 166.969 0.000
314 H16 h1 E 313 312 311 1.075 107.412 -79.237 0.000
315 H16 h1 E 313 312 311 1.072 112.718 45.831 0.000
316 C82 c3 3 313 312 311 1.546 105.501 168.183 0.000
317 H16 h1 E 316 313 312 1.078 112.223 43.267 0.000
318 H16 h1 E 316 313 312 1.111 103.348 -72.572 0.000
319 N35 n3 B 316 313 312 1.474 111.750 171.265 0.000
320 H16 hn E 319 316 313 1.012 109.774 58.501 0.000
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Received on Mon Feb 16 2004 - 21:53:00 PST
