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seq2itp
- Norbert
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12 years 10 months ago #732
by Norbert
seq2itp was created by Norbert
Dear All,
How can I use the seq2itp.pl script to generate a MARTINI coarse grained topology for a transmembrane peptide containing a neutral aspartate?
Thank you very much
Norbert
How can I use the seq2itp.pl script to generate a MARTINI coarse grained topology for a transmembrane peptide containing a neutral aspartate?
Thank you very much
Norbert
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- xavier
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12 years 10 months ago #734
by xavier
For the neutral type of the Glu and Asp, we use parameters for the Gln and Asn respectively. You'll have to edit the protein itp file given as output, locate the Asp and adjust the bead type of the side chain of the Asp (Qa) the one of a Asn (P5). You should also change the charge indicated at the end of the line ... Alternatively you can change the name of the ASP to ASN and the atomic names also to the ones of an Asp directly in the pdb file.
The first solution is quicker.
XAvier.
XAvier.
Replied by xavier on topic seq2itp
Norbert wrote: Dear All,
How can I use the seq2itp.pl script to generate a MARTINI coarse grained topology for a transmembrane peptide containing a neutral aspartate?
Thank you very much
Norbert
For the neutral type of the Glu and Asp, we use parameters for the Gln and Asn respectively. You'll have to edit the protein itp file given as output, locate the Asp and adjust the bead type of the side chain of the Asp (Qa) the one of a Asn (P5). You should also change the charge indicated at the end of the line ... Alternatively you can change the name of the ASP to ASN and the atomic names also to the ones of an Asp directly in the pdb file.
The first solution is quicker.
XAvier.
XAvier.
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- jantunes
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12 years 5 months ago #820
by jantunes
Hey,
Sorry to bug, but in Martini: Extension to Proteins and martini_v2.1_aminoacids.itp there are proper transformations for Glu and Asp neutral forms, just trading GLU to GLU0 (and ASP to ASP0), the charge -1 to 0 and Q to P1/P3 (respectively). So I don't understand your answer.
Correct me if I'm mistaken, please! :)
Cumps,
Jorge
Replied by jantunes on topic seq2itp
xavier wrote:
For the neutral type of the Glu and Asp, we use parameters for the Gln and Asn respectively. You'll have to edit the protein itp file given as output, locate the Asp and adjust the bead type of the side chain of the Asp (Qa) the one of a Asn (P5).
XAvier.
Hey,
Sorry to bug, but in Martini: Extension to Proteins and martini_v2.1_aminoacids.itp there are proper transformations for Glu and Asp neutral forms, just trading GLU to GLU0 (and ASP to ASP0), the charge -1 to 0 and Q to P1/P3 (respectively). So I don't understand your answer.
Correct me if I'm mistaken, please! :)
Cumps,
Jorge
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- xavier
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12 years 5 months ago #821
by xavier
Dear Jorge,
Thanks for pointing out my mistake! I overlook the similarity of GLN/ASN and neutral GLU/ASP ... you are correct :))
Best,
XAvier.
Replied by xavier on topic seq2itp
jantunes wrote:
xavier wrote:
For the neutral type of the Glu and Asp, we use parameters for the Gln and Asn respectively. You'll have to edit the protein itp file given as output, locate the Asp and adjust the bead type of the side chain of the Asp (Qa) the one of a Asn (P5).
XAvier.
Hey,
Sorry to bug, but in Martini: Extension to Proteins and martini_v2.1_aminoacids.itp there are proper transformations for Glu and Asp neutral forms, just trading GLU to GLU0 (and ASP to ASP0), the charge -1 to 0 and Q to P1/P3 (respectively). So I don't understand your answer.
Correct me if I'm mistaken, please! :)
Cumps,
Jorge
Dear Jorge,
Thanks for pointing out my mistake! I overlook the similarity of GLN/ASN and neutral GLU/ASP ... you are correct :))
Best,
XAvier.
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