From: mashaojie163 (mashao_jie_at_163.com)
Date: Sat Nov 17 2007 - 01:28:51 CST
Dear Sir:
Thank your for response. I do it accoording to what you said. However, I find that there are large difference of TIP3p water parameters between cornell_all.prm and par_all27_prot_lipid.inp.
The parameterrs of TIP3P water in cornell_all.prm as following:
BONDS
OW HW 553.0 0.9572 ! TIP3P water
HW HW 553.0 1.5136 ! TIP3P water
THETAS
HW OW HW 100. 104.52 ! TIP3P water
NONBONDED NBXMOD 5 GROUP SWITCH CDIEL -
CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 0.83333333 WMIN 1.4
HW 0.0 -0.0000 0.6000 0.0 -0.0000 0.6000 ! TIP3P water model
OW 0.0 -0.1520 1.7683 0.0 -0.0760 1.7683 ! TIP3P water model
The parameterrs of TIP3P water in par_all27_prot_lipid.inp as following:
BONDS
OT HT 450.000 0.9572 ! ALLOW WAT
! FROM TIPS3P GEOM
HT HT 0.000 1.5139 ! ALLOW WAT
! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
ANGLES
HT OT HT 55.000 104.5200 ! ALLOW WAT
! TIP3P GEOMETRY, ADM JR.
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
HT 0.000000 -0.046000 0.224500 ! ALLOW WAT
!TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
OT 0.000000 -0.152100 1.768200 ! ALLOW WAT
!TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
They are both TIP3P water, why does the large difference exist?
1) I note that the K of bond HT-HT is 0 in charmm forcefield, it means we do not need to add the HT-HT bond in simulation with shake, but the bond can not to be neglected if we use amber field with shake.
2) I node that epson of HW is 0.0 in amber forcefield,which is different HT in charmm force field. It mean there are no VDW interaction between H atom and other atom. Is it right??
Best Regards
**************************************************
Shaojie Ma
Institute of Nano Science
Nanjing University of Aeronautics and Astronautics
mashaojie_at_nuaa.edu.cn
Nanjing 210016, China
**************************************************
----- Original Message -----
From: Floris Buelens
To: mashaojie163 ; namd-l
Sent: Friday, November 16, 2007 7:19 PM
Subject: Re: namd-l: howcan I use amber forcefield in NAMD?
Hi,
there is a way to do this without leap or antechamber using the two files you refer to, and you're working along the right lines. You're correct in changing the 'parameters' item in your .conf file to the cornell_all.prm. However, you also need to generate your psf using the cornell_all.rtf topology definition file - you need to change the 'toplogy' line in your psfgen input to point to this file, eg 'topology /home/masj/data/namd/common/cornell_all.rtf'. If you absolutely need these amber parameters this is a perfectly correct way of doing it, but as other users suggested it might not be the best choice, particularly since as far as I'm aware the amber parameters in those files are pretty old (1994 or so...),
good luck
Floris Buelens
Department of Crystallography, Birkbeck College, London
----- Original Message ----
From: mashaojie163 <mashao_jie_at_163.com>
To: Irene Newhouse <einew_at_hotmail.com>; namd-l <namd-l_at_ks.uiuc.edu>
Sent: Friday, 16 November, 2007 2:55:53 AM
Subject: Re: namd-l: howcan I use amber forcefield in NAMD?
Dear Irene Newhouse:
Thank you for your quick response. Why can not I use the two file? I just do a test calculation for a water box.
1) I replace atom type "HT" and "OT" in my charmm psf into "HW" and "OW", which is consisent with cornell_all.prm.
2) I change
paraTypeCharmm on
parameters /home/masj/data/namd/common/par_all27_prot_lipid.inp
as
paraTypeCharmm on
parameters /home/masj/data/namd/common/cornell_all.prm
I run the configure file and every thing seems OK! Why can not I use the parameter file directly??
----- Original Message -----
From: Irene Newhouse
To: mashaojie163
Sent: Friday, November 16, 2007 1:22 AM
Subject: RE: namd-l: howcan I use amber forcefield in NAMD?
No you can't! You must have a prmtop file & an inpcrd file. AMBER's input is very different from CHARMM. In CHARMM you use a utility to generate a psf file - UIUC provides it as a standalone or a VMD plugin, containing topology information only, and then NAMD itself uses it, the parm file & a pdb file for the original coordinates. AMBER creates a prmtop file that COMBINES the topology AND those portions of the parameter file needed for your particular system AND a file containing coordinates only that replaces the pdb file CHARMM uses. In order to make it easier for AMBER users to switch, NAMD kept this input style. However, they did not make any effort to supply their own utility to create these files, as they did with CHARMM. Therefore you have to use tleap or xleap from AMBER. Is there no one where you work who has an AMBER you can borrow for this?
Irene
From: mashao_jie_at_163.com
To: einew_at_hotmail.com; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: howcan I use amber forcefield in NAMD?
Date: Thu, 15 Nov 2007 20:23:49 +0800
Dear Irene Newhouse:
Thank you for your quick response. I don not have amber. I find there are two file in the directory amber9.ffparms\dat\amberff_in_charmm\ cornell_all.prm and cornell_all.rtf. It seems that the two file is charmm format of amber field. Can I use it directly? Can I use cornell_all.rtf to create psf file and then use cornell_all.prm as parameter file to conduct my calculation?
----- Original Message -----
From: Irene Newhouse
To: mashaojie163 ; namd-l_at_ks.uiuc.edu
Sent: Thursday, November 15, 2007 2:51 PM
Subject: RE: namd-l: howcan I use amber forcefield in NAMD?
When you use the AMBER forcefield with NAMD, you will not have a psf file. That is CHARMM-style. You will have a prmtop file and an inpcrd file. The easiest way to generate these is by using tleap, which is a utility that comes with AMBER9, and only with AMBER9. The good news is that the academic price for AMBER is very reasonable. Instructions for using tleap can be found in the AMBER documentation. You create these files from a pdb input file. You can use xleap, a GUI version of tleap, to build proteins, too, but I've never tried that.
The parameter files come with AMBER. You want to use ff99SB, which better simulates alpha-helical sections of protein than ff99. [That will make sense once you start looking at how to use tleap].
VMD can display prmtop & inpcrd files in a way similar to pdb/psf combinations. When you animate a dcd file computed with AMBER input with NAMD, you use the prmtop file in the same way as a psf file.
Once you get hold of AMBER, write me off-line if you run into trouble & I'll try to help you out.
Irene Newhouse
> From: mashao_jie_at_163.com
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: howcan I use amber forcefield in NAMD?
> Date: Thu, 15 Nov 2007 11:58:39 +0800
>
> Dear Sir:
> How can I use amber force field to calculate protein.
> I think that I should do this according to the following 3 steps.
>
> 1) I should generate a psf file and a coord file. Which top file should be used to gererate the psf file? Where can I download the topfile? What type is the coord file?? Is PDB OK??
>
> 2) I should have a amber parameter file. Which parameter file should I choose? Where can I download the parameter file??
>
> 3) I should modify the configure file acoording
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html.
> then I run NAMD.
>
>
> So, there are so many questions before I excute the 3rd step. Please help me and answer the questions in detail! Thank you very much??
> Best Regards
> **************************************************
> Shaojie Ma
> Institute of Nano Science
> Nanjing University of Aeronautics and Astronautics
> mashaojie_at_nuaa.edu.cn
> Nanjing 210016, China
> **************************************************
>
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