On 21/04/2012 9:27 PM, rama david wrote:
Hi Gromacs Friends,
I wish to apply charmff 27 to my protein and ligand
I proceed in following way ..
1. I separate the protein and ligand by grep command
then delete the ligand lne grom pdb file
2 I generate the topology of protein in gromacs
using the pdb2gmx command
3 I generate the ligand topology by swissparam ,
4 I protein top , I added the line..
; Include ligand topology
#include "ligand.itp"
The ligand.itp generated by swissparam contain position restrain file in it
Ligand itp has following line.....
1 CR 1 LIG C1 1 0.0000 12.0110
2 CR 1 LIG C2 2 0.0000 12.0110
3 CR 1 LIG C3 3 0.0000 12.0110
4 CR 1 LIG C4 4 0.0000 12.0110
5 CR 1 LIG C5 5 0.0000 12.0110
6 CR 1 LIG C6 6 0.0000 12.0110
7 CR 1 LIG CM 7 0.5030 12.0110
8 NRP 1 LIG N 8 -0.8530 14.0067
9 HNRP 1 LIG HN1 9 0.4500 1.0079
10 HNRP 1 LIG HN2 10 0.4500 1.0079
11 HNRP 1 LIG HN3 11 0.4500 1.0079
12 HCMM 1 LIG H1 12 0.0000 1.0079
13 HCMM 1 LIG H22 13 0.0000 1.0079
14 HCMM 1 LIG H23 14 0.0000 1.0079
15 HCMM 1 LIG H32 15 0.0000 1.0079
16 HCMM 1 LIG H33 16 0.0000 1.0079
17 HCMM 1 LIG H42 17 0.0000 1.0079
18 HCMM 1 LIG H43 18 0.0000 1.0079
19 HCMM 1 LIG H52 19 0.0000 1.0079
20 HCMM 1 LIG H53 20 0.0000 1.0079
21 HCMM 1 LIG H62 21 0.0000 1.0079
22 HCMM 1 LIG H63 22 0.0000 1.0079
23 HCMM 1 LIG HM2 23 0.0000 1.0079
24 HCMM 1 LIG HM3 24 0.0000 1.0079
.
.
.
Now when I give the grompp command I stuck with following error ...
Program grompp, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/toppush.c, line: 1166
Fatal error:
Atomtype CR not found
The atomtype CR used in ligand .itp corresponds to no [atomtype] entry
in the standard force field, so grompp is stuck. You need to find out
why SwissParam thinks this is a reasonable atom type to use, and adapt
your solution accordingly.
Mark
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