[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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