|
Hi all:
I built a topol file for tip5p water accordint
to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr
file, three errors came even the system just have one tip5p
water.
The error is :
ERROR 1 [file "topol.top", line
10]:
atom OW <Res SOL-1> has mass
0
ERROR 2 [file "topol.top", line
10]:
atom HW1 <Res SOL-1> has mass
0
ERROR 3 [file "topol.top", line
10]:
atom HW2 <Res SOL-1> has mass
0 In fact, the mass for all above atoms were all
defined in atp file. How can i fix it? Thanks a lot.
The build steps are follows:
1. Named the atom type in new tip5p.itp.
Add them to ffG53a6.atp and ffG53a6nb.itp.
In tip5p.itp:
[ atoms ]
; id at type res nr residu name at name cg nr charge 1 5p_O 1 SOL OW 1 0 2 5p_H 1 SOL HW1 1 0.241 3 5p_H 1 SOL HW2 1 0.241 4 5p_L 1 SOL OL1 1 -0.241 5 5p_L 1 SOL OL2 1 -0.241 In ffG53a6.atp
5p_O 15.99940
; O TIP5P Water
5p_H 1.00800 ; H TIP5P Water 5p_L 0.00000 ; L TIP5P Water In ffG53a6nb.itp
5p_O
8 0.000 0.000 A
2.470013e-03 2.278383e-06
5p_H 1 0.000 0.000 A 0 0 5p_L 0 0.000 0.000 D 0 0 2. Write top file.
#include "ffG53a6.itp"
#include "tip5p_.itp" [ system ]
; Name Protein [ molecules ]
; Compound #mols SOL 1 3. Built gro
5
1SOL OW 1 0.321 1.614 0.603 1SOL HW1 2 0.377 1.643 0.675 1SOL HW2 3 0.258 1.555 0.645 1SOL OL1 4 0.358 1.581 0.554 1SOL OL2 5 0.288 1.669 0.574 0.5 0.5 0.5 4. grompp -f em.mdp Then the errors came.
*************************************************
Ji Qing Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ，82618423 ************************************************* |
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