amber 里面怎么修改力场啊
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解决时间 2021-03-24 00:21
- 提问者网友：骑士
- 2021-03-23 11:06
amber 里面怎么修改力场啊
最佳答案
- 五星知识达人网友：像个废品
- 2021-03-23 12:33
AMBER修改残基
4-Hydroxyl-Proline (PR4)
Step 1:
Prepare two mol2 files: alpha and beta conformatons for ACE-PR4-ACE (Take a look at the molecular structure )
Step 2:
Generate two gaussian input files: alpha and beta using the following antechamber command:
antechamber -fi mol2 -fo gzmat -i pro4a.mol2 -o pro4a.gau
antechamber -fi mol2 -fo gzmat -i pro4b.mol2 -o pro4b.gau
Do the following modifications on pro4a.gau and pro4b.gau:
change opt to popt in the keyword section
freeze t19 and t21 during the minimization with a tag of "F"
Step 3:
Run gaussian to get two output files: alpha and beta
Step 4:
Extract ESP files from gaussian output files ( alpha and beta ) and merge them togetherpro4.esp ; then prepare input files for two-stage resp fitting ( Step I and Stage II ); finally run resp program to get resp charge ( Pro4.crg ).
espgen -i pro4a.out -o pro4a.esp
espgen -i pro4b.out -o pro4b.esp
cat pro4a.esp pro4b.esp >pro4.esp
respgen -i pro4a.mol2 -o pro4-step1.respin -f resp1 respgen -i pro4a.mol2 -o pro4-step2.respin -f resp2
Manually revision pro4-step1.respin and pro4-step2.respin are necessary in this example since respgen cannot generate input files for multiple molecules.
Step 5:
Load pro4.crg and generate an ac file ( pro4.ac ).
antechamber -fi mol2 -fo ac -i pro4a.mol2 -o pro4.ac -c rc -cf pro4.crg
However, if one only use one conformation, he may generate an ac file from the gaussian output file with charge method tag set to "resp" directly.
Step 6:
Read in pro4.ac and a mainchain defination file mainchain.pro4 to generate prep input file 4-OH-PROfor 4-OH-PRO.
In mainchain defination file, HEAD_NAME is the atom connected to the immediately previous residue and TAIL_NAME is the atom connected to the immediately behide reside; OMIT_NAME(s) is (are) not a part of the residue, however they are necessary to maintain a proper chemical environment; MAINCHAIN are mainchain atoms (HEAD_NAME and TAIL_NAME are mainchain atoms automatically); PRE_HEAD_TYPE and POST_TAIL_TYPE N are the atom types of atoms in other residues that are connected to the head and tail, respectively. CHARGE is the net charge of the residue in question.
prepgen -i pro4.ac -o pro4.prepi -f prepi -m mainchain.pro4 -rn PR4 -rf pro4.res
For PR4 , HEAD_NAME is N1; TAIL_NAME is C7 and all the atoms in green and yellow are omitted atoms. The PRO_HEAD_TYPE and POST_TAIL_TYPE are C and N respectively
Step 7:
With pro4.prepi, one may use leap to generate topolgy files for sander etc. Here we generate atopology file for ALA-PRO4-ALA with leap.
loadamberprep pro4.prep
aa =sequence {ALA PR4 ALA}
saveamberparm aa ala-pr4-ala.prmtop ala-pr4-ala.prmcrd
4-Hydroxyl-Proline (PR4)
Step 1:
Prepare two mol2 files: alpha and beta conformatons for ACE-PR4-ACE (Take a look at the molecular structure )
Step 2:
Generate two gaussian input files: alpha and beta using the following antechamber command:
antechamber -fi mol2 -fo gzmat -i pro4a.mol2 -o pro4a.gau
antechamber -fi mol2 -fo gzmat -i pro4b.mol2 -o pro4b.gau
Do the following modifications on pro4a.gau and pro4b.gau:
change opt to popt in the keyword section
freeze t19 and t21 during the minimization with a tag of "F"
Step 3:
Run gaussian to get two output files: alpha and beta
Step 4:
Extract ESP files from gaussian output files ( alpha and beta ) and merge them togetherpro4.esp ; then prepare input files for two-stage resp fitting ( Step I and Stage II ); finally run resp program to get resp charge ( Pro4.crg ).
espgen -i pro4a.out -o pro4a.esp
espgen -i pro4b.out -o pro4b.esp
cat pro4a.esp pro4b.esp >pro4.esp
respgen -i pro4a.mol2 -o pro4-step1.respin -f resp1 respgen -i pro4a.mol2 -o pro4-step2.respin -f resp2
Manually revision pro4-step1.respin and pro4-step2.respin are necessary in this example since respgen cannot generate input files for multiple molecules.
Step 5:
Load pro4.crg and generate an ac file ( pro4.ac ).
antechamber -fi mol2 -fo ac -i pro4a.mol2 -o pro4.ac -c rc -cf pro4.crg
However, if one only use one conformation, he may generate an ac file from the gaussian output file with charge method tag set to "resp" directly.
Step 6:
Read in pro4.ac and a mainchain defination file mainchain.pro4 to generate prep input file 4-OH-PROfor 4-OH-PRO.
In mainchain defination file, HEAD_NAME is the atom connected to the immediately previous residue and TAIL_NAME is the atom connected to the immediately behide reside; OMIT_NAME(s) is (are) not a part of the residue, however they are necessary to maintain a proper chemical environment; MAINCHAIN are mainchain atoms (HEAD_NAME and TAIL_NAME are mainchain atoms automatically); PRE_HEAD_TYPE and POST_TAIL_TYPE N are the atom types of atoms in other residues that are connected to the head and tail, respectively. CHARGE is the net charge of the residue in question.
prepgen -i pro4.ac -o pro4.prepi -f prepi -m mainchain.pro4 -rn PR4 -rf pro4.res
For PR4 , HEAD_NAME is N1; TAIL_NAME is C7 and all the atoms in green and yellow are omitted atoms. The PRO_HEAD_TYPE and POST_TAIL_TYPE are C and N respectively
Step 7:
With pro4.prepi, one may use leap to generate topolgy files for sander etc. Here we generate atopology file for ALA-PRO4-ALA with leap.
loadamberprep pro4.prep
aa =sequence {ALA PR4 ALA}
saveamberparm aa ala-pr4-ala.prmtop ala-pr4-ala.prmcrd
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