From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Dec 13 2010 - 13:14:40 CST
pdbalias residue atomname1 atomname2
You'd also find this in the PSFgen manual here: http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
However, that's not your problem. The problem is you haven't yet patched your termini. The atom names LEU293 is for an amidated C-terminus and those for GLU351 correspond to an acetylated N-terminus. This appears to be backwards though - 293 is your C-terminus and 351 is your N-terminus! In any case, to apply such terminal patches, you would add lines like "first ACE" and "last CT2" within your segment command.
On Dec 11, 2010, at 2:56 PM, Christian Jorgensen wrote:
> 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:51 CST