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SCN & SCP vs SCD in martini2.2P FF, using martini
- visvaldas
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10 years 4 months ago #3026
by visvaldas
SCN & SCP vs SCD in martini2.2P FF, using martini was created by visvaldas
Hi,
I processed a protein using martinize.py (Martini2.2FF) , and grompp gives an error about nonmatching atom names, always SCN or SCP vs. SCN.
For example, let's take atom 6. Topology file says:
[ atoms ]
1 Qd 1 MET BB 1 1.0000 ; C
2 C5 1 MET SC1 2 0.0000 ; C
3 P5 2 GLY BB 3 0.0000 ; C
4 P5 3 GLU BB 4 0.0000 ; C
5 Qa 3 GLU SC1 5 0.0000 36.0000 ; C
6 D 3 GLU SCN 6 -1.0000 36.0000 ; C
But PDB file reads:
ATOM 1 BB MET A 1 -24.881 -9.057 22.377 1.00 0.00
ATOM 2 SC1 MET A 1 -27.588 -5.989 21.381 1.00 0.00
ATOM 3 BB GLY A 2 -25.611 -9.645 25.039 1.00 0.00
ATOM 4 BB GLU A 3 -25.904 -11.623 27.401 1.00 0.00
ATOM 5 SC1 GLU A 3 -23.300 -11.526 30.569 1.00 0.00
ATOM 6 SCD GLU A 3 -23.196 -11.546 30.542 1.00 0.00
Looking at martinize.py sorce code, I can see that this is because of a dummy atom. I could replace manually all atom names
in pdb file to match the top file. But before doing that, I probably better ask if it is safe to do, in order not to mess things up.
Best regards,
Visvaldas
I processed a protein using martinize.py (Martini2.2FF) , and grompp gives an error about nonmatching atom names, always SCN or SCP vs. SCN.
For example, let's take atom 6. Topology file says:
[ atoms ]
1 Qd 1 MET BB 1 1.0000 ; C
2 C5 1 MET SC1 2 0.0000 ; C
3 P5 2 GLY BB 3 0.0000 ; C
4 P5 3 GLU BB 4 0.0000 ; C
5 Qa 3 GLU SC1 5 0.0000 36.0000 ; C
6 D 3 GLU SCN 6 -1.0000 36.0000 ; C
But PDB file reads:
ATOM 1 BB MET A 1 -24.881 -9.057 22.377 1.00 0.00
ATOM 2 SC1 MET A 1 -27.588 -5.989 21.381 1.00 0.00
ATOM 3 BB GLY A 2 -25.611 -9.645 25.039 1.00 0.00
ATOM 4 BB GLU A 3 -25.904 -11.623 27.401 1.00 0.00
ATOM 5 SC1 GLU A 3 -23.300 -11.526 30.569 1.00 0.00
ATOM 6 SCD GLU A 3 -23.196 -11.546 30.542 1.00 0.00
Looking at martinize.py sorce code, I can see that this is because of a dummy atom. I could replace manually all atom names
in pdb file to match the top file. But before doing that, I probably better ask if it is safe to do, in order not to mess things up.
Best regards,
Visvaldas
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- Clement
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10 years 4 months ago - 10 years 4 months ago #3044
by Clement
Replied by Clement on topic SCN & SCP vs SCD in martini2.2P FF, using martini
grompp gives you a warning (by that I mean it's not a fatal error); you can ignore it by adding the -maxwarn flag. The atom names from the topology will be used.
Last edit: 10 years 4 months ago by Clement.
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9 years 10 months ago - 9 years 10 months ago #3873
by zhiyue
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Replied by zhiyue on topic SCN & SCP vs SCD in martini2.2P FF, using martini
I got into the same problem. My question is, how can I replace all these SCD's with SCP or SCN correspondlingly?
Thanks in advance.
Best
Thanks in advance.
Best
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Last edit: 9 years 10 months ago by zhiyue.
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9 years 10 months ago #3874
by zhiyue
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Replied by zhiyue on topic SCN & SCP vs SCD in martini2.2P FF, using martini
Can I replace all SCP and SCN in *.itp with SCD? By doing this atom names in *.itp and *.gro match. It's not convenient to do the opposite way. I don't think atom names matter as long as atom types are correct. Correct me if I was wrong. Thanks.
Best
Best
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
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9 years 10 months ago #3875
by Clement
Replied by Clement on topic SCN & SCP vs SCD in martini2.2P FF, using martini
The only moment moment it matters is when creating the .tpr file; then the names from the .itp file will be used if the -maxwarn flag is used correctly. Atom (or residue) names are not important at all. The only "codes" you need to keep in the .itp files are the bead types.
But remember any .gro file can be re-generated at any time; .itp files are more complicated... Convenient or not, I'd play with the .gro file before modifying .itp.
But remember any .gro file can be re-generated at any time; .itp files are more complicated... Convenient or not, I'd play with the .gro file before modifying .itp.
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9 years 10 months ago #3876
by zhiyue
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Replied by zhiyue on topic SCN & SCP vs SCD in martini2.2P FF, using martini
Hi Clement,
Thanks for your advice! I have some additional questions.
1. How does this mismatch problem occur, i.e., martinize.py generates SCD while grompp gives SCP and SCN?
2. Is there any convenient way to midify *.gro files other than manually correction?
Best
Thanks for your advice! I have some additional questions.
1. How does this mismatch problem occur, i.e., martinize.py generates SCD while grompp gives SCP and SCN?
2. Is there any convenient way to midify *.gro files other than manually correction?
Best
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
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9 years 10 months ago - 9 years 10 months ago #3877
by Clement
Cause things haven't been written at the same time... Constant development here. And as I said earlier, names have absolutely NO importance. You could name your beads A B C D ... , it wouldn't change your simulation, would it? ;-)
(Hu)midify, never easy. :-P
Why do you need to modify the initial .gro file? It will be automatically modified (using the names from the .itp) and rewritten in all the output .gro files you'll generate. Otherwise, I guess some clever replacement with sed or equivalent would work.
Replied by Clement on topic SCN & SCP vs SCD in martini2.2P FF, using martini
zhiyue wrote: 1. How does this mismatch problem occur, i.e., martinize.py generates SCD while grompp gives SCP and SCN?
Cause things haven't been written at the same time... Constant development here. And as I said earlier, names have absolutely NO importance. You could name your beads A B C D ... , it wouldn't change your simulation, would it? ;-)
zhiyue wrote: 2. Is there any convenient way to midify *.gro files other than manually correction?
(Hu)midify, never easy. :-P
Why do you need to modify the initial .gro file? It will be automatically modified (using the names from the .itp) and rewritten in all the output .gro files you'll generate. Otherwise, I guess some clever replacement with sed or equivalent would work.
Last edit: 9 years 10 months ago by Clement.
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