主月 ：） wrote:
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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put the mass in your tip5p.itp file.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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