AMBER Archive (2004)

Subject: Re: AMBER: TER in amber

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Fri Feb 13 2004 - 02:35:41 CST

Did you try as I suggested with "ambpdb -p topfile -aatm < crdfile >
pdbfile"?
Did you get the same thing??? Did you get NMET instead of MET? The TER
card is still there?
You can gzip your topfile and the crd file and Send them as attachements
directly to my email ...not to the list...
vlad

Lishan Yao wrote:

>Actually MET is the begining of the second monomer.
>
>Lishan
>
>On Thu, 2004-02-12 at 10:56, Vlad Cojocaru wrote:
>
>
>>Something strange appears in your pdb:
>>
>>ATOM 2422 N MET 159 57.187 49.344 8.302
>>ATOM 2423 H1 MET 159 58.164 49.404 8.550
>>ATOM 2424 H2 MET 159 56.749 49.930 8.998
>>ATOM 2425 H3 MET 159 57.049 49.830 7.427
>>
>>I dont really understand whta is with H1 H2 H3 atoms ..which I think should not be there. You also miss the H atom from MET. Did you check that you top and crd files are correct when you create the pdb? I use ambpdb a lot and I do not have any problem with it. If I where you I would load the top and crd file into a program that reads them (ex. VMD) and check what's up with MET 159 and identify the atoms....and compare them with the standard amber MET residue. But to me this looks like the MET is of N terminal type...
>>Did you try to use ambpdb with -aatm option and without -bres option ...then you will get amber names both for res and atoms and if you see an NMET 159 instead of MET 159 you have to correct that in Leap.
>>Hope this helps
>>vlad
>>
>>
>>
>>Lishan Yao wrote:
>>
>>
>>
>>>I use ambpdb to convert a restrt file to a pdb file. If you look at the
>>>pdb file I get, it is kind of strange because ambpdb put TER inside
>>>MET159. It's supposed to be between GLU158 and MET159. The protein is a
>>>dimer, 158 residues for each monomer. Then I checked the structure, the
>>>rmsd between MD trajectory and crystal structure is fine, about 1 ang.
>>>Is it a bug or something?
>>>
>>>..........
>>>ATOM 2406 N GLU 158 36.434 53.530 17.579
>>>ATOM 2407 H GLU 158 35.540 53.140 17.843
>>>ATOM 2408 CA GLU 158 36.697 53.794 16.144
>>>ATOM 2409 HA GLU 158 37.390 53.038 15.774
>>>ATOM 2410 CB GLU 158 35.446 53.739 15.324
>>>ATOM 2411 2HB GLU 158 34.712 54.507 15.570
>>>ATOM 2412 3HB GLU 158 35.742 54.035 14.318
>>>ATOM 2413 CG GLU 158 34.768 52.396 15.325
>>>ATOM 2414 2HG GLU 158 34.414 52.137 16.323
>>>ATOM 2415 3HG GLU 158 33.855 52.471 14.735
>>>ATOM 2416 CD GLU 158 35.616 51.243 14.745
>>>ATOM 2417 OE1 GLU 158 36.318 50.563 15.478
>>>ATOM 2418 OE2 GLU 158 35.517 50.983 13.521
>>>ATOM 2419 C GLU 158 37.331 55.181 15.770
>>>ATOM 2420 O GLU 158 38.509 55.258 15.446
>>>ATOM 2421 OXT GLU 158 36.647 56.223 15.912
>>>ATOM 2422 N MET 159 57.187 49.344 8.302
>>>ATOM 2423 H1 MET 159 58.164 49.404 8.550
>>>ATOM 2424 H2 MET 159 56.749 49.930 8.998
>>>ATOM 2425 H3 MET 159 57.049 49.830 7.427
>>>TER
>>>ATOM 2426 CA MET 159 56.759 47.930 8.261
>>>ATOM 2427 HA MET 159 55.672 47.924 8.186
>>>ATOM 2428 CB MET 159 57.302 47.188 7.059
>>>ATOM 2429 2HB MET 159 57.181 46.119 7.237
>>>ATOM 2430 3HB MET 159 56.777 47.521 6.163
>>>ATOM 2431 CG MET 159 58.769 47.282 6.818
>>>ATOM 2432 2HG MET 159 59.243 47.481 7.780
>>>ATOM 2433 3HG MET 159 58.914 46.273 6.432
>>>ATOM 2434 SD MET 159 59.306 48.648 5.829
>>>ATOM 2435 CE MET 159 61.028 48.239 5.783
>>>ATOM 2436 1HE MET 159 61.399 48.021 6.784
>>>ATOM 2437 2HE MET 159 61.062 47.360 5.139
>>>ATOM 2438 3HE MET 159 61.561 49.085 5.350
>>>ATOM 2439 C MET 159 57.279 47.251 9.593
>>>ATOM 2440 O MET 159 58.409 47.411 10.022
>>>.......
>>>
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>>>
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-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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