Nilesh Dhumal wrote:
I have total 256 water molecules. I am trying to genrate the .top file
from .pdb so I used pdb2gmx.
pdb2gmx is only really useful for building topologies for linear molecules built
from repeat building blocks, not for systems of individual molecules.
How can I genrate the .top file with pdb2gmx for 256 water molecules.
With a text editor:
#include "ffoplsaa.itp"
#include "spc_fw.itp"
[ system ]
water
[ molecules ]
WAT 256
-Justin
Nilesh
On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to run a simulation for flexiable water. I use the
parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing
changes.
I addes "WAT" as a new residue name in aminoacids.dat
I addred two atom times in ffoplsaa.atp
opls_1001 15.99940 ; O SPC_fw Water opls_1002 1.00800 ; H SPC_fw
Water
I added following parameters in ffoplsaa.rtp
[ WAT]
[ atoms ]
OWA opls_1001 -0.82 1
HWA1 opls_1002 0.41 2
HWA2 opls_1002 0.41 2
[ bonds ]
OWA HWA1
OWA HWA2
I made a spc_fw.itp file.
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_1001 OWA 8 15.99940 -0.820 A 3.1655e-01
6.503e-01
opls_1002 HWA 1 1.00800 0.410 A 0.00e+00 0.00e+00
[ bondtypes ]
; i j func b0 kb
OWA HWA 1 0.1012 443153.3808 ; J. Chem. Phys.
(2006),124,024503
[ angletypes ]
; i j k func th0 cth
HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys.
(2006),124,024503
[ moleculetype ]
; Name nrexcl
WAT 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB 1 opls_1001 1 WAT OWA 1
-0.82
2 opls_1002 1 WAT HWA1 1 0.41
3 opls_1002 1 WAT HWA2 1 0.41
[ bonds ]
; i j funct
1 2 1
1 3 1
[ angles ]
; i j k funct
2 1 3 1
Finally I made changes in ffoplsaa.itp file
;#include "ffoplsaanb.itp"
;#include "ffoplsaabon.itp"
#include "spc_fw.itp"
#include "spc_fw_mol.itp"
For pdb2gmx
pdb2gmx -f water.pdb -o water.pdb -p water.top -ter
I get following error
Fatal error:
Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms
while sorting atoms
WHy is reading HOH residue. In my pdb file I mentioned WAT as residure.
How can I fix this error?
If I recall, pdb2gmx does some internal translations to standardize water
nomenclature. In reality, you don't need pdb2gmx at all - you've
already shown that you're created a topology for the water model.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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