balaji nagarajan wrote:
Dear Users !
I have a problem in generating the topology of the attached molecule as pdb.
earlier i have done using the same pdb for solvating the structure using
spc and spce water box ,
there was no such error when i do for TIP4P and oplsaa force field i got
the error
as follows
---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 523
Fatal error:
number of coordinates in coordinate file (1AKI_solv.gro, 4164)
does not match topology (topol.top, 5527)
I used the following lines to do that
pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
You told pdb2gmx to write the TIP4P topology into your .top, but then you used a
3-point water model. You need to solvate with tip4p.gro.
-Justin
grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
mdrun -v -deffnm em
in the grompp it says the error , how to solve this , and it comes only
for tip4p not for other water models.
thanks in advance
--
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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