Ravi Kumar Venkatraman wrote:
Dear All,
To remove water of crystallization from pdb files. I
removed following things from pdb file.
REMARK 3 SOLVENT ATOMS : 78
.............................................................
.............................................................
HETATM 1072 O HOH A 199 16.684 13.594 -5.832 0.31
18.51 O
HETATM 1073 O HOH A 200 27.534 38.059 -12.862 0.48
18.19 O
HETATM 1074 O HOH A 201 25.892 35.973 11.563 0.46
18.15 O
HETATM 1075 O HOH A 202 24.790 25.182 16.063 0.46
17.64 O
HETATM 1076 O HOH A 203 12.580 21.214 5.006 0.51
17.97 O
HETATM 1077 O HOH A 204 19.687 23.750 -4.851 0.37
18.08 O
HETATM 1078 O HOH A 205 27.098 35.956 -12.358 0.39
18.71 O
HETATM 1079 O HOH A 206 37.255 9.634 10.002 0.46
18.39 O
HETATM 1080 O HOH A 207 43.755 23.843 8.038 0.38
17.96 O
CONECT 48 981
CONECT 238 889
CONECT 513 630
CONECT 601 724
CONECT 630 513
CONECT 724 601
CONECT 889 238
CONECT 981 48
Is this right or I have to delete some other things also.
The only lines you absolutely must remove are the coordinate entries. REMARK
and CONECT lines are ignored by pdb2gmx and most other Gromacs programs.
-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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