[gmx-users] Replicating monomer units-problem with geometry of connecting atoms
Moeed
lecielll at googlemail.com
Fri Jun 25 20:07:34 CEST 2010
Hello Justin,
I think I did not convey my problem properly in the former message. Please
help me with the following 2 questions:
I am actually having problem with geometry of C atoms at the end of one
monomer unit and C at the beginning of the next unit. I am trying to
replicate 4-carbon monomer. The C s on the backbone have sp3 geometry but
when I put the second unit after the first, 4th and 5th dont have sp3
geometry. Before I said I got the 1.53A bond distance between C 4 and 5 by
changing the box size by try and error and you mentioned, there should be no
try and error. I guess you thought I am talking bout C s on the chain. Since
structure is tetrahedral it is not like that I specify the the gap between
the molecule and wall by taking into account just the half of the bond
length. Apart from the distance, I have no control on the angle between C 4
and 5 either. Replicating using genconf does not give right geometry for
connecting C atoms.
Q1- So actually I was asking you if there is any way to set a proper bond
length and angle between 4-C repeating units since I am doing this by
changing the box size. When connecting atoms ( C 4 and 5 in case of first
and second repeating units) get close I am not getting the 110 angle ( this
is actually the angle between carbons on the chain).
What I do is:
editconf -f 4C.pdb -o 4C430.gro -box 0.430 -bt cubic
genconf -f 4C430.gro -o 4C430rep.gro -nbox 5 1 1
4C430.gro:
4
1Eth C1 1 0.392 0.194 0.291
1Eth C2 2 0.276 0.174 0.193
1Eth C3 3 0.154 0.255 0.237
1Eth C4 4 0.037 0.237 0.140
0.43000 0.43000 0.43000
5 boxes replicated: and renamed the residues 1 and last.
4C430rep.gro
20
1EthB C1 1 0.392 0.194 0.291 0.0000 0.0000 0.0000
1EthB C2 2 0.276 0.174 0.193 0.0000 0.0000 0.0000
1EthB C3 3 0.154 0.255 0.237 0.0000 0.0000 0.0000
1EthB C4 4 0.037 0.237 0.140 0.0000 0.0000 0.0000
2Eth C1 5 0.822 0.194 0.291 0.0000 0.0000 0.0000
2Eth C2 6 0.706 0.174 0.193 0.0000 0.0000 0.0000
2Eth C3 7 0.584 0.255 0.237 0.0000 0.0000 0.0000
2Eth C4 8 0.467 0.237 0.140 0.0000 0.0000 0.0000
3Eth C1 9 1.252 0.194 0.291 0.0000 0.0000 0.0000
3Eth C2 10 1.136 0.174 0.193 0.0000 0.0000 0.0000
3Eth C3 11 1.014 0.255 0.237 0.0000 0.0000 0.0000
3Eth C4 12 0.897 0.237 0.140 0.0000 0.0000 0.0000
4Eth C1 13 1.682 0.194 0.291 0.0000 0.0000 0.0000
4Eth C2 14 1.566 0.174 0.193 0.0000 0.0000 0.0000
4Eth C3 15 1.444 0.255 0.237 0.0000 0.0000 0.0000
4Eth C4 16 1.327 0.237 0.140 0.0000 0.0000 0.0000
5EthE C1 17 2.112 0.194 0.291 0.0000 0.0000 0.0000
5EthE C2 18 1.996 0.174 0.193 0.0000 0.0000 0.0000
5EthE C3 19 1.874 0.255 0.237 0.0000 0.0000 0.0000
5EthE C4 20 1.757 0.237 0.140 0.0000 0.0000 0.0000
2.15000 0.43000 0.43000
with rtp file:
; Polyethylene - this is an internal residue
[ Eth ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_136 -0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_136 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
[ bonds ]
C1 -C4
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 +C1
; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ EthB ]
[ atoms ]
C1 opls_135 -0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
H13 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_136 -0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_136 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
[ bonds ]
C1 H11
C1 H12
C1 H13
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 +C1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_136 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_136 -0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_136 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
H43 opls_140 0.060 4
[ bonds ]
C1 -C4
C1 H11
C1 H12
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 H43
and with hdb file:
Eth 4
2 6 H1 C1 C2 -C4
2 6 H2 C2 C1 +C1
2 6 H3 C3 C2 +C1
2 6 H4 C4 C3 +C1
EthB 4
3 4 H1 C1 C2 +C1
2 6 H2 C2 C1 +C1
2 6 H3 C3 C2 +C1
2 6 H4 C4 C3 +C1
EthE 4
2 6 H1 C1 C2 -C4
2 6 H2 C2 C1 -C4
2 6 H3 C3 C2 -C4
3 4 H4 C4 C3 -C4
then:
pdb2gmx -f 4C430rep.gro -o 4C430repgmx.gro -p 4C430repgmx.top -ff oplsaa >&
output.pdb2gmx
Q2- What I am getting is a top file but gro file processed with hdb and rtp
gives a very weird structure which has nothing to do with PE chain.
Thanks for your attention.
Moeed
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