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  5. About the force field (dppc.itp) currently treated

normal About the force field (dppc.itp) currently treated

  • Yuki
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10 years 5 months ago #2533 by Yuki
About the force field (dppc.itp) currently treated was created by Yuki
Hi All,

It is a question about "dppc.itp" contained in "rev_trans.tar.gz" of Reverse transformation.
The file of lipid molecules other(dmpc,popc,pope etc..) than "dppc.itp" is looked for.
Please let me know the download place.

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10 years 5 months ago - 10 years 5 months ago #2538 by Clement
Replied by Clement on topic About the force field (dppc.itp) currently treated
I understand you want to perform reverse transformation on another type of lipids than DPPC. And you need... atomistic or coarse-grained topologies? The coarse-grained topologies can be found here ; the atomistic topologies most probably in the Lipibook .

Have you considered this reverse transformation method ?

Good luck.
Last edit: 10 years 5 months ago by Clement.

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10 years 5 months ago #2606 by Yuki
Replied by Yuki on topic About the force field (dppc.itp) currently treated
Thank you very much for your responses.

One more question.
For the test, from Lipidbook, the structure of DPPC was downloaded by 43A1-s3, and one lipid molecule and a force field file were obtained.
I added the mapping data (description below "#ifdef DPPCPOSRES") of "dppc.itp"(A) take from the tutorial to "dppc.itp"(B).
Next, I created the topology file of all the atoms and coarse graining.
When I tried to read and changed by fg2cg, the following errors were displayed and I was not able to change.

Please give me advice as to what to do.

----contents of the error
Fatal error:
Invalid order for directive atomtypes, file ""ffg43A1-S3_02.itp"", line 1
<<<fg_dppc.top>>>
#include "ffG43A1-S3_02.itp"
#include "dppc.itp"

[ system ]
DPPC single

[ molecules ]
DPPC 1
<<<cg_dppc.top>>>

#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"

[ system ]
DPPC LIPOSOME

[ molecules ]
DPPC 1

--file in a directory --
dppc-structure.gro
fg_dppc.top
cg_dppc.top
dppc.itp (B)
ffG43A1-S3_02.itp
martini_v2.1.itp
martini_v2.0_lipids.itp

*dppc.itp
(A)by rev_trans.tar.gz
(B)by GROMOS43A1-S3-DPPC-oliver-v1.zip

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10 years 5 months ago #2607 by Clement
Replied by Clement on topic About the force field (dppc.itp) currently treated
The error seems to come from the file defining the GROMOS 43a1 force field; are you sure this file includes everything needed for an atomistic simulation? From where was this file downloaded?

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10 years 5 months ago #2817 by Yuki
Replied by Yuki on topic About the force field (dppc.itp) currently treated
Im sorry for late reply.

It has changed by rewriting force field for lipid molecules (by Lipidbook) according to 43a2 force field (by tutorial).

Thank you for giving advice.

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  1. Force Fields
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  5. About the force field (dppc.itp) currently treated
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