From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Fri Aug 18 2006 - 02:11:11 CDT
Hi all
I am trying to do LES with namd. when i am adding "multiply 5 P"
command in psfgen script then i am getting a pdb file like this and when i
am trying to run the simulation, it says "bad global exclusion count"
ATOM 6916 C PRO X2002 12.102 48.868 47.649 1.00 1.00 P
C
ATOM 6917 C PRO X2002 12.102 48.868 47.649 1.00 2.00 P
C
ATOM 6918 C PRO X2002 12.102 48.868 47.649 1.00 3.00 P
C
ATOM 6919 C PRO X2002 12.102 48.868 47.649 1.00 4.00 P
C
ATOM 6920 C PRO X2002 12.102 48.868 47.649 1.00 5.00 P
C
ATOM 6921 OT1 PRO X2002 13.049 48.707 47.927 0.00 1.00 P
O
ATOM 6922 OT1 PRO X2002 13.049 48.707 47.927 0.00 2.00 P
O
ATOM 6923 OT1 PRO X2002 13.049 48.707 47.927 0.00 3.00 P
O
ATOM 6924 OT1 PRO X2002 13.049 48.707 47.927 0.00 4.00 P
O
ATOM 6925 OT1 PRO X2002 13.049 48.707 47.927 0.00 5.00 P
O
ATOM 6926 OT2 PRO X2002 11.554 49.258 46.909 0.00 1.00 P
O
ATOM 6927 OT2 PRO X2002 11.554 49.258 46.909 0.00 2.00 P
O
ATOM 6928 OT2 PRO X2002 11.554 49.258 46.909 0.00 3.00 P
O
ATOM 6929 OT2 PRO X2002 11.554 49.258 46.909 0.00 4.00 P
O
ATOM 6930 OT2 PRO X2002 11.554 49.258 46.909 0.00 5.00 P
O
ATOM 6931 N PRO X2002 11.897 47.752 49.839 1.00 1.00 P
N
ATOM 6932 N PRO X2002 11.897 47.752 49.839 1.00 2.00 P
N
ATOM 6933 N PRO X2002 11.897 47.752 49.839 1.00 3.00 P
N
ATOM 6934 N PRO X2002 11.897 47.752 49.839 1.00 4.00 P
N
ATOM 6935 N PRO X2002 11.897 47.752 49.839 1.00 5.00 P
N
ATOM 6936 HN1 PRO X2002 12.820 47.521 49.531 0.00 1.00 P
H
ATOM 6937 HN1 PRO X2002 12.820 47.521 49.531 0.00 2.00 P
H
ATOM 6938 HN1 PRO X2002 12.820 47.521 49.531 0.00 3.00 P
H
ATOM 6939 HN1 PRO X2002 12.820 47.521 49.531 0.00 4.00 P
H
ATOM 6940 HN1 PRO X2002 12.820 47.521 49.531 0.00 5.00 P
H
ATOM 6941 HN2 PRO X2002 11.423 46.927 50.147 0.00 1.00 P
H
ATOM 6942 HN2 PRO X2002 11.423 46.927 50.147 0.00 2.00 P
H
ATOM 6943 HN2 PRO X2002 11.423 46.927 50.147 0.00 3.00 P
H
ATOM 6944 HN2 PRO X2002 11.423 46.927 50.147 0.00 4.00 P
H
ATOM 6945 HN2 PRO X2002 11.423 46.927 50.147 0.00 5.00 P
H
ATOM 6946 CD PRO X2002 11.970 48.693 50.911 1.00 1.00 P
C
ATOM 6947 CD PRO X2002 11.970 48.693 50.911 1.00 2.00 P
C
ATOM 6948 CD PRO X2002 11.970 48.693 50.911 1.00 3.00 P
C
ATOM 6949 CD PRO X2002 11.970 48.693 50.911 1.00 4.00 P
C
ATOM 6950 CD PRO X2002 11.970 48.693 50.911 1.00 5.00 P
C
ATOM 6951 HD1 PRO X2002 11.425 48.151 51.717 0.00 1.00 P
H
ATOM 6952 HD1 PRO X2002 11.425 48.151 51.717 0.00 2.00 P
H
ATOM 6953 HD1 PRO X2002 11.425 48.151 51.717 0.00 3.00 P
H
ATOM 6954 HD1 PRO X2002 11.425 48.151 51.717 0.00 4.00 P
H
ATOM 6955 HD1 PRO X2002 11.425 48.151 51.717 0.00 5.00 P
H
ATOM 6956 HD2 PRO X2002 12.972 49.022 51.271 0.00 1.00 P
H
ATOM 6957 HD2 PRO X2002 12.972 49.022 51.271 0.00 2.00 P
H
ATOM 6958 HD2 PRO X2002 12.972 49.022 51.271 0.00 3.00 P
H
ATOM 6959 HD2 PRO X2002 12.972 49.022 51.271 0.00 4.00 P
H
ATOM 6960 HD2 PRO X2002 12.972 49.022 51.271 0.00 5.00 P
H
ATOM 6961 CA PRO X2002 11.164 48.331 48.736 1.00 1.00 P
C
ATOM 6962 CA PRO X2002 11.164 48.331 48.736 1.00 2.00 P
C
ATOM 6963 CA PRO X2002 11.164 48.331 48.736 1.00 3.00 P
C
ATOM 6964 CA PRO X2002 11.164 48.331 48.736 1.00 4.00 P
C
ATOM 6965 CA PRO X2002 11.164 48.331 48.736 1.00 5.00 P
C
ATOM 6966 HA PRO X2002 10.498 47.597 48.298 0.00 1.00 P
H
ATOM 6967 HA PRO X2002 10.498 47.597 48.298 0.00 2.00 P
H
ATOM 6968 HA PRO X2002 10.498 47.597 48.298 0.00 3.00 P
H
ATOM 6969 HA PRO X2002 10.498 47.597 48.298 0.00 4.00 P
H
ATOM 6970 HA PRO X2002 10.498 47.597 48.298 0.00 5.00 P
H
ATOM 6971 CB PRO X2002 10.342 49.445 49.274 1.00 1.00 P
C
ATOM 6972 CB PRO X2002 10.342 49.445 49.274 1.00 2.00 P
C
ATOM 6973 CB PRO X2002 10.342 49.445 49.274 1.00 3.00 P
C
ATOM 6974 CB PRO X2002 10.342 49.445 49.274 1.00 4.00 P
C
ATOM 6975 CB PRO X2002 10.342 49.445 49.274 1.00 5.00 P
C
ATOM 6976 HB1 PRO X2002 9.385 49.033 49.665 0.00 1.00 P
H
ATOM 6977 HB1 PRO X2002 9.385 49.033 49.665 0.00 2.00 P
H
ATOM 6978 HB1 PRO X2002 9.385 49.033 49.665 0.00 3.00 P
H
ATOM 6979 HB1 PRO X2002 9.385 49.033 49.665 0.00 4.00 P
H
ATOM 6980 HB1 PRO X2002 9.385 49.033 49.665 0.00 5.00 P
H
ATOM 6981 HB2 PRO X2002 10.117 50.218 48.512 0.00 1.00 P
H
ATOM 6982 HB2 PRO X2002 10.117 50.218 48.512 0.00 2.00 P
H
ATOM 6983 HB2 PRO X2002 10.117 50.218 48.512 0.00 3.00 P
H
ATOM 6984 HB2 PRO X2002 10.117 50.218 48.512 0.00 4.00 P
H
ATOM 6985 HB2 PRO X2002 10.117 50.218 48.512 0.00 5.00 P
H
ATOM 6986 CG PRO X2002 11.153 49.908 50.448 1.00 1.00 P
C
ATOM 6987 CG PRO X2002 11.153 49.908 50.448 1.00 2.00 P
C
ATOM 6988 CG PRO X2002 11.153 49.908 50.448 1.00 3.00 P
C
ATOM 6989 CG PRO X2002 11.153 49.908 50.448 1.00 4.00 P
C
ATOM 6990 CG PRO X2002 11.153 49.908 50.448 1.00 5.00 P
C
ATOM 6991 HG1 PRO X2002 10.547 50.437 51.209 0.00 1.00 P
H
ATOM 6992 HG1 PRO X2002 10.547 50.437 51.209 0.00 2.00 P
H
ATOM 6993 HG1 PRO X2002 10.547 50.437 51.209 0.00 3.00 P
H
ATOM 6994 HG1 PRO X2002 10.547 50.437 51.209 0.00 4.00 P
H
ATOM 6995 HG1 PRO X2002 10.547 50.437 51.209 0.00 5.00 P
H
ATOM 6996 HG2 PRO X2002 11.967 50.579 50.090 0.00 1.00 P
H
ATOM 6997 HG2 PRO X2002 11.967 50.579 50.090 0.00 2.00 P
H
ATOM 6998 HG2 PRO X2002 11.967 50.579 50.090 0.00 3.00 P
H
ATOM 6999 HG2 PRO X2002 11.967 50.579 50.090 0.00 4.00 P
H
ATOM 7000 HG2 PRO X2002 11.967 50.579 50.090 0.00 5.00 P
H
but without multiply command it is showing pdb file like
ATOM 6916 C PRO X2002 12.102 48.868 47.649 1.00 0.00 P
C
ATOM 6917 OT1 PRO X2002 13.049 48.707 47.927 0.00 0.00 P
O
ATOM 6918 OT2 PRO X2002 11.554 49.258 46.909 0.00 0.00 P
O
ATOM 6919 N PRO X2002 11.897 47.752 49.839 1.00 0.00 P
N
ATOM 6920 HN1 PRO X2002 12.820 47.521 49.531 0.00 0.00 P
H
ATOM 6921 HN2 PRO X2002 11.423 46.927 50.147 0.00 0.00 P
H
ATOM 6922 CD PRO X2002 11.970 48.693 50.911 1.00 0.00 P
C
ATOM 6923 HD1 PRO X2002 11.425 48.151 51.717 0.00 0.00 P
H
ATOM 6924 HD2 PRO X2002 12.972 49.022 51.271 0.00 0.00 P
H
ATOM 6925 CA PRO X2002 11.164 48.331 48.736 1.00 0.00 P
C
ATOM 6926 HA PRO X2002 10.498 47.597 48.298 0.00 0.00 P
H
ATOM 6927 CB PRO X2002 10.342 49.445 49.274 1.00 0.00 P
C
ATOM 6928 HB1 PRO X2002 9.385 49.033 49.665 0.00 0.00 P
H
ATOM 6929 HB2 PRO X2002 10.117 50.218 48.512 0.00 0.00 P
H
ATOM 6930 CG PRO X2002 11.153 49.908 50.448 1.00 0.00 P
C
ATOM 6931 HG1 PRO X2002 10.547 50.437 51.209 0.00 0.00 P
H
ATOM 6932 HG2 PRO X2002 11.967 50.579 50.090 0.00 0.00 P
H
when i am writing 5 in column B instead of 0.00 manually, then i am able to
run the simulation.
what is the problem with my psfgen script? if i am replacing 0.00 with my
LES factor in pdb file, am i doing something wrong or its ok. my psfgen
script is
package require psfgen
topology top_all27_prot_lipid.inp
topology fad_top.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {pdb chain_A.pdb}
coordpdb chain_A.pdb A
segment B {pdb chain_B.pdb}
coordpdb chain_B.pdb B
segment F {pdb FAD.pdb}
coordpdb FAD.pdb F
segment P {
pdb pro.pdb
}
coordpdb pro.pdb P
guesscoord
multiply 5 P # i have also tried P:2002 but got same result.
writepdb prodh3.pdb
writepsf prodh3.psf
exit
thanks for your help.
-- Dhiraj Kumar Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153
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