Hi,
Are you certain that residues 4, 5, and 6 in your original topology
aren't water? If you want, send me (off-list) the topology and restart
you are using and I will see if I can reproduce the behavior.
-Dan
On Fri, Oct 25, 2019 at 1:58 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
>
> Dear Amber
> I have a dipeptide and water system in which I put dipeptide twice for free
> energy calculation.
> >From the combined coordinate file I want to extract pdb files of both
> dipeptide and water separately following the scheme mentioned in amber
> tutorial for free energy:
> http://ambermd.org/tutorials/advanced/tutorial9/#overview
> I am running following in cpptraj:-
>
> $cpptraj -p ${s}_vdw_bonded.parm7 <<_EOF
> trajin ${s}_prepare/press.rst7
>
> # remove the peptides and keep the rest
> strip ":1,2,3,4,5,6"
> outtraj ${s}_wateronly.pdb onlyframes 1
>
> # extract the 2nd peptide & water
> unstrip
> strip ":4,5,6,7-999999" (4,5,6 are residues for peptide)
> outtraj ${s}_ala1.pdb onlyframes 1
>
> # extract the 1st peptide & water
> unstrip
> strip ":1,2,3,7-999999" (4,5,6 are residues for peptide)
> outtraj ${s}_ala0.pdb onlyframes 1
>
> However
> I am getting 1 pdb correct (having 1,2,3) residues but other pdb only shows
> water (4,5,6) as mentioned below:-
>
> protein_ala1:-
> CRYST1 22.538 24.635 21.053 90.00 90.00 90.00 1
> ATOM 1 HH31 ACE 1 9.249 8.608 11.725 1.00 0.00
> H
> ATOM 2 CH3 ACE 1 9.350 9.581 11.245 1.00 0.00
> C
> ATOM 3 HH32 ACE 1 8.600 10.227 11.702 1.00 0.00
> H
> ATOM 4 HH33 ACE 1 9.073 9.437 10.200 1.00 0.00
> H
> ATOM 5 C ACE 1 10.779 10.051 11.266 1.00 0.00
> C
> ATOM 6 O ACE 1 11.743 9.323 11.528 1.00 0.00
> O
> ATOM 7 N ALA 2 10.874 11.327 11.027 1.00 0.00
> N
> ATOM 8 H ALA 2 9.999 11.784 10.813 1.00 0.00
> H
> ATOM 9 CA ALA 2 12.142 12.067 10.917 1.00 0.00
> C
> ATOM 10 HA ALA 2 12.715 11.733 11.781 1.00 0.00
> H
> ATOM 11 CB ALA 2 12.737 11.744 9.517 1.00 0.00
> C
> ATOM 12 HB1 ALA 2 12.202 12.133 8.650 1.00 0.00
> H
> ATOM 13 HB2 ALA 2 13.651 12.338 9.552 1.00 0.00
> H
> ATOM 14 HB3 ALA 2 12.969 10.695 9.337 1.00 0.00
> H
> ATOM 15 C ALA 2 11.973 13.590 11.120 1.00 0.00
> C
> ATOM 16 O ALA 2 10.865 14.123 11.245 1.00 0.00
> O
> ATOM 17 N NME 3 13.122 14.313 11.150 1.00 0.00
> N
> ATOM 18 H NME 3 14.008 13.835 11.072 1.00 0.00
> H
> ATOM 19 CH3 NME 3 13.129 15.733 11.121 1.00 0.00
> C
> ATOM 20 HH31 NME 3 12.462 16.093 11.904 1.00 0.00
> H
> ATOM 21 HH32 NME 3 14.043 16.213 11.470 1.00 0.00
> H
> ATOM 22 HH33 NME 3 12.827 16.142 10.157 1.00 0.00
> H
> TER 23 NME 3
> END
> protein_ala0:-
> CRYST1 22.538 24.635 21.053 90.00 90.00 90.00 1
> ATOM 1 O WAT 4 14.970 17.297 19.845 1.00 0.00
> O
> ATOM 2 H1 WAT 4 14.645 18.039 19.334 1.00 0.00
> H
> ATOM 3 H2 WAT 4 15.167 17.667 20.706 1.00 0.00
> H
> TER 4 WAT 4
> ATOM 4 O WAT 5 6.951 19.773 7.005 1.00 0.00
> O
> ATOM 5 H1 WAT 5 6.880 18.832 6.845 1.00 0.00
> H
> ATOM 6 H2 WAT 5 6.207 20.152 6.536 1.00 0.00
> H
> TER 7 WAT 5
> ATOM 7 O WAT 6 6.808 18.228 9.602 1.00 0.00
> O
> ATOM 8 H1 WAT 6 7.407 18.576 10.262 1.00 0.00
> H
> ATOM 9 H2 WAT 6 6.919 18.806 8.848 1.00 0.00
> H
> TER 10 WAT 6
> END
>
> Please suggest me where I am doing wrong?
> thanks in advance
> Sadaf
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Received on Tue Nov 12 2019 - 06:00:03 PST
