Problem when using psfgen

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Sat Dec 11 2010 - 14:56:06 CST

Hi all,
I am encountering a problem wherein when I use the psfgen on my system certain atoms are left out because the PDB and topology are using different naming conventions

ERROR
reading coordinates from pdb file prot.pdb for segment SEG
Warning: failed to set coordinate for atom NT LEU:293 SEG
Warning: failed to set coordinate for atom HT1 LEU:293 SEG
Warning: failed to set coordinate for atom HT2 LEU:293 SEG
Warning: failed to set coordinate for atom CAY GLU:351 SEG
Warning: failed to set coordinate for atom HY1 GLU:351 SEG
Warning: failed to set coordinate for atom HY2 GLU:351 SEG
Warning: failed to set coordinate for atom HY3 GLU:351 SEG
Warning: failed to set coordinate for atom CY GLU:351 SEG
Warning: failed to set coordinate for atom OY GLU:351 SEG

E.g. for residue LEU293: NT, HT1, HT2 are not included in the residue LEU entry in the topology file.

pdb entry for LEU
ATOM 1451 C LEU U 293 -3.904 -4.100 17.814 0.00 0.00 U3
ATOM 1452 O LEU U 293 -3.257 -3.297 18.518 0.00 0.00 U3
ATOM 1453 NT LEU U 293 -5.187 -4.323 18.232 0.00 0.00 U3
ATOM 1454 HT1 LEU U 293 -5.381 -3.879 19.106 0.00 0.00 U3
ATOM 1455 HT2 LEU U 293 -5.895 -4.776 17.689 0.00 0.00 U3
ATOM 1456 N LEU U 293 -2.315 -4.185 15.942 0.00 0.00 U3
ATOM 1457 HN LEU U 293 -1.461 -4.354 16.428 0.00 0.00 U3
ATOM 1458 CA LEU U 293 -3.480 -4.791 16.534 0.00 0.00 U3
ATOM 1459 HA LEU U 293 -4.272 -4.612 15.823 0.00 0.00 U3
ATOM 1460 CB LEU U 293 -3.238 -6.254 16.841 0.00 0.00 U3
ATOM 1461 HB1 LEU U 293 -4.040 -6.849 17.328 0.00 0.00 U3
ATOM 1462 HB2 LEU U 293 -2.999 -6.788 15.897 0.00 0.00 U3
ATOM 1463 CG LEU U 293 -2.029 -6.620 17.740 0.00 0.00 U3
ATOM 1464 HG LEU U 293 -1.068 -6.309 17.277 0.00 0.00 U3
ATOM 1465 CD1 LEU U 293 -2.110 -6.157 19.160 0.00 0.00 U3
ATOM 1466 HD11 LEU U 293 -3.145 -6.437 19.454 0.00 0.00 U3
ATOM 1467 HD12 LEU U 293 -1.386 -6.643 19.849 0.00 0.00 U3
ATOM 1468 HD13 LEU U 293 -1.911 -5.074 19.311 0.00 0.00 U3
ATOM 1469 CD2 LEU U 293 -1.787 -8.145 17.826 0.00 0.00 U3
ATOM 1470 HD21 LEU U 293 -2.717 -8.557 18.271 0.00 0.00 U3
ATOM 1471 HD22 LEU U 293 -1.627 -8.591 16.821 0.00 0.00 U3
ATOM 1472 HD23 LEU U 293 -0.998 -8.353 18.580 0.00 0.00 U3

topology entry for LEU
RESI LEU 0.00
GROUP
ATOM N NH1 -0.47 ! | HD11 HD12
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 CD1--HD13
ATOM HA HB 0.09 ! | | /
GROUP ! HA-CA--CB--CG-HG
ATOM CB CT2 -0.18 ! | | \
ATOM HB1 HA 0.09 ! | HB2 CD2--HD23
ATOM HB2 HA 0.09 ! O=C | \
GROUP ! | HD21 HD22
ATOM CG CT1 -0.09
ATOM HG HA 0.09
GROUP
ATOM CD1 CT3 -0.27
ATOM HD11 HA 0.09
ATOM HD12 HA 0.09
ATOM HD13 HA 0.09
GROUP
ATOM CD2 CT3 -0.27
ATOM HD21 HA 0.09
ATOM HD22 HA 0.09
ATOM HD23 HA 0.09

My question: I have read that one can use a pdbalias for these atoms so that they will be found in the topology file, any ideas on how this would be done?
could this be pdbalias NT N ?

thank you very much
Christian

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