From: emilia wu (emilia.l.wu_at_gmail.com)
Date: Thu Jul 02 2009 - 18:35:32 CDT
Hi all,
I want to run a md simulation for a small peptide with 13 amino acid, there
is an unnatural amino acid, just add another CH3 group on the side chain of
Trp4.
I modified the topology file of charmm top_all27_prot_na.rtf, and add this
part. the red one is modified part from TRP.
RESI W4M 0.00
GROUP
ATOM N NH1 -0.47 ! | HE3
ATOM HN H 0.31 ! HN-N |
ATOM CA CT1 0.07 ! | HB1 CE3
ATOM HA HB 0.09 ! | | / \\
GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3
ATOM CB CT2 -0.18 ! | | || || |
ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2
ATOM HB2 HA 0.09 ! O=C / \ / \ //
GROUP ! | HD1 NE1 CZ2
ATOM CG CY -0.03 ! | |
ATOM CD1 CA 0.035 ! CM1 HZ2
ATOM HD1 HP 0.115 / | \
ATOM NE1 NY -0.61 HM1 HM2 HM3
ATOM CM1 CT3 0.11
ATOM HM1 HA 0.09
ATOM HM2 HA 0.09
ATOM HM3 HA 0.09
ATOM CE2 CPT 0.13
ATOM CD2 CPT -0.02
GROUP
ATOM CE3 CA -0.115
ATOM HE3 HP 0.115
GROUP
ATOM CZ3 CA -0.115
ATOM HZ3 HP 0.115
GROUP
ATOM CZ2 CA -0.115
ATOM HZ2 HP 0.115
GROUP
ATOM CH2 CA -0.115
ATOM HH2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG NE1 CD1
BOND CZ2 CE2
BOND N HN N CA C CA C +N
BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1
BOND CB HB2 CD1 HD1 NE1 CM1 CE3 HE3 CZ2 HZ2
BOND CZ3 HZ3 CH2 HH2
BOND CM1 HM1 CM1 HM2 CM1 HM3
DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
After I modified the topology file, I use psfgen to read the pdb file, but
it gave this message:
ERROR! Explicit exclusions or fluctuating charges not supported, atom
ignored.
ERROR! Explicit exclusions or fluctuating charges not supported, atom
ignored.
what does this mean, what should I do?
I notice even if I did not read this unnatural amino acid, the error is
still there only if the topology file was changed.
Thanks in advance!
Emilia
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