Dear francois,
This is great, I also got advantage from your answer. Thank you very much.
regards
Setyanto
On Tue, Mar 6, 2012 at 4:48 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Maxier,
>
> > Does anyone have a PREP file and/or a frcmod file for ammonium,
> > NH4+? I will appreciate any information regarding the parameters for
>
> - I created a PDB file for NH4+ using xLEaP
> ATOM 1 N1 NH4 1 0.000 0.000 0.000 1.00 0.00
> ATOM 2 H11 NH4 1 1.000 0.000 0.000 1.00 0.00
> ATOM 3 H12 NH4 1 -0.334 0.943 0.000 1.00 0.00
> ATOM 4 H13 NH4 1 -0.334 -0.472 0.816 1.00 0.00
> ATOM 5 H14 NH4 1 -0.334 -0.472 -0.816 1.00 0.00
>
> - To exchange data between R.E.D. Server users, see:
> http://q4md-forcefieldtools.org/REDS/faq.php#21
>
> - I executed R.E.D. Server/Ante_R.E.D. 2.0 (using the public account):
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFzzqfBsVbADFDaWoMB8GYUr0fz775ttrO0/P6811.html
> A P2N file is generated:
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFzzqfBsVbADFDaWoMB8GYUr0fz775ttrO0/P6811/Mol_antered1-out.p2n
> See the corresponding java applet:
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFzzqfBsVbADFDaWoMB8GYUr0fz775ttrO0/P6811/javaappletp2n-1.html
>
> - I modified the header of the P2N file:
> REMARK TITLE NH4+
> REMARK CHARGE-VALUE 1
> REMARK MULTIPLICITY-VALUE 1
>
> - Using the P2N file, I executed R.E.D. Server/R.E.D. IV:
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFH2Az2ADFx2ADFkADFimzs5YwGDAIXxbxGUcADF0/P6812.html
> A mol2 file is generated:
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFH2Az2ADFx2ADFkADFimzs5YwGDAIXxbxGUcADF0/P6812/Data-R.E.D.Server/Mol_m1-o1.mol2
> See the corresponding java applet:
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFH2Az2ADFx2ADFkADFimzs5YwGDAIXxbxGUcADF0/P6812/javaappletmol2-1.html
>
> - You can use the following LEaP script to define the FF atom types:
> NH4 = loadmol2 Mol_m1-o1.mol2
> set NH4 name "NH4"
> # head & tail not needed since whole molecule
> # connect0 & connect1 not needed since whole molecule
> set NH4.1 restype solvent
> set NH4.1 name "NH4"
> # set FF atom types
> set NH4.1.N1 type N3
> set NH4.1.H11 type H
> set NH4.1.H12 type H
> set NH4.1.H13 type H
> set NH4.1.H14 type H
> # See http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
> savemol2 NH4 Mol_m1-o1-bis.mol2 1
>
> - no missing force field parameter should be found by LEaP
>
> regards, Francois
>
> PS
> There is a rounding off error of 2.10-4 e in the mol2 file generated
> by R.E.D. IV; you might use the "Re_fit" mode of R.E.D. III.51 and set
> $COR_CHR = "5" to make this error = 0.
> See http://q4md-forcefieldtools.org/RED/HowTo-III.5.pdf page 6.
> # charge values at 1.10-4 e
> > NH4 = loadmol2 Mol_m1-o1.mol2
> Loading Mol2 file: ./Mol_m1-o1.mol2
> Reading MOLECULE named NH4
> > charge NH4
> Total unperturbed charge: 0.999800
> Total perturbed charge: 0.999800
> # charge values at 1.10-5 e
> > NH4 = loadmol2 Mol_m1-o1.mol2
> Loading Mol2 file: ./Mol_m1-o1.mol2
> Reading MOLECULE named NH4
> > charge NH4
> Total unperturbed charge: 1.000000
> Total perturbed charge: 1.000000
>
> .<TRIPOS>MOLECULE
> NH4
> 5 4 1 0 1
> SMALL
> USER_CHARGES
> .<TRIPOS>ATOM
> 1 N1 0.000000 -0.000000 -0.000000 N3 1 NH4
> -0.72096
> 2 H11 0.000000 -0.029732 1.013003 H 1 NH4
> 0.43024
> 3 H12 0.000000 0.964979 -0.309636 H 1 NH4
> 0.43024
> 4 H13 -0.827470 -0.467624 -0.351683 H 1 NH4
> 0.43024
> 5 H14 0.827470 -0.467624 -0.351683 H 1 NH4
> 0.43024
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 1 4 1
> 4 1 5 1
> .<TRIPOS>SUBSTRUCTURE
> 1 NH4 1 **** 0 **** ****
>
>
>
>
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Received on Wed Mar 07 2012 - 21:30:04 PST
