Dear AMBER Users,
Id like to run MD simulation for cytochrome complex, but I am puzzled with
the HEM force field. I want to make topology file and coordinate file of
oxo-iron- thiolate group of Cys as the fashion of HEM. I tried to use
the hem_ryd.in
and frcmod.hemryd files from *P. Rydberg, L. Olsen, P.-O. Norrby, and U.
Ryde *in the article *A general transition-state force field for cytochrome
P450 hydroxylation*
http://pubs.acs.org/doi/abs/10.1021/ct700110f
It failed to read the files.
I chose ff99SB as the force field, the commands I used in tleap are as
follows:
tleap f leaprc.ff99SB
> source leaprc.gaff
> loadamberprep hem_ryd.in
Loading Prep file: ./hem_ryd.in
)nexpected EOF: discarding residue (\par
> loadamberparams frcmod.hemryd
Loading parameters: ./frcmod.hemryd
Reading force field modification type file (frcmod)
Reading title:
{\rtf1\ansi\ansicpg936\deff0\deflang1033\deflangfe2052{\fonttbl{\f0\fnil\fprq2\fcharset134
.\'cb\'ce\'cc\'e5;}}
Unknown keyword: {\*\genera in parameter file.
Unknown keyword: in cytochr in parameter file.
Unknown keyword: \par
in parameter file.
ERROR: \par: mass not read - omitting
ERROR: BOND\par: mass not read - omitting
ERROR: \par: mass not read - omitting
ERROR: ANGLE\par: mass not read - omitting
WARNING: NP-FE-NP: polarization 180.000000
WARNING: NO-FE-NO: polarization 180.000000
WARNING: NO-FE-NP: polarization 84.134000
WARNING: FE-NP-Cc: polarization 125.896000
WARNING: FE-NO-Cc: polarization 125.896000
WARNING: NO-Cc-Cb: polarization 111.117000
WARNING: NP-Cc-Cb: polarization 111.117000
WARNING: NO-Cc-Cd: polarization 123.587000
WARNING: NP-Cc-Cd: polarization 123.587000
WARNING: Cc-NP-Cc: polarization 110.979000
WARNING: Cc-NO-Cc: polarization 110.979000
WARNING: Cc-Cb-Cb: polarization 108.287000
WARNING: Cc-Cd-Cc: polarization 125.062000
WARNING: Cb-Cc-Cd: polarization 127.159000
WARNING: Cc-Cd-HA: polarization 116.824000
WARNING: OQ-HQ-c3: polarization 171.358000
WARNING: SQ-FE-OQ: polarization 181.694000
WARNING: Cc-Cb-HA: polarization 125.283000
WARNING: HA-Cb-Cb: polarization 128.727000
WARNING: NO-FE-SQ: polarization 89.406000
WARNING: NO-FE-OQ: polarization 91.640000
WARNING: NP-FE-SQ: polarization 89.406000
WARNING: NP-FE-OQ: polarization 91.640000
WARNING: FE-OQ-HQ: polarization 121.332000
WARNING: FE-SQ-CT: polarization 107.918000
WARNING: H1-CT-SQ: polarization 110.169000
WARNING: HQ-c3-hc: polarization 100.239000
WARNING: c3-c3-HQ: polarization 102.202000
WARNING: HQ-c3-c2: polarization 102.266000
WARNING: HQ-c3-h1: polarization 102.691000
WARNING: f-c3-HQ: polarization 106.355000
WARNING: HQ-c3-n3: polarization 106.509000
WARNING: HQ-c3-os: polarization 106.783000
WARNING: HQ-c3-ca: polarization 106.753000
WARNING: HQ-c3-ss: polarization 105.815000
WARNING: HQ-c3-nh: polarization 109.690000
WARNING: HQ-c3-c: polarization 100.720000
ERROR: \par: mass not read - omitting
ERROR: DIHEDRAL\par: mass not read - omitting
WARNING: X-Cc-Cb-X: polarization 16.746000
ERROR: \par: mass not read - omitting
ERROR: IMPROPER\par: mass not read - omitting
ERROR: c3-ha-c: mass not read - omitting
ERROR: ca-o: mass not read - omitting
ERROR: \par: mass not read - omitting
ERROR: NONBON\par: mass not read - omitting
ERROR: CH3SCH3: mass not read - omitting
ERROR: }: mass not read - omitting
>
I have attached the hem_ryd.in and frcmod.hemryd files
Can someone suggest me how I should modify the files?
Also, is there anyone who use this fashion of HEM, and successfully ran
Amber with the provided heme forcefield, may I ask which forcefield do you
choose?
Best regards,
Cuiyl
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Received on Fri Jun 15 2012 - 05:30:03 PDT
