CHARMM Development Project Forums User Discussion & Questions General Chemistry Discussions Which software can build correct pdb for CHARMM

Dear all,
Recently,I tried InsightII to build dsDNA(CAGT-CAGT-CAGT)
.But there are much error in the pdb file form InsightII .And
I tried the softwares "SYBYL , Spartan ...". I still can't build
correct pdb file for charmm.I just change the wrong type by my finger.Could someone tell me which software can get it or
send me the script fixing wrong odb file ?
thank you
yeng-tseng

See io.doc

Try the VML-software which is free on the net, or the following lines in your CHARMM-input file:

TRANSLATE TYPE "atom1" "CHARMM-atom1"
...
...
...
TRANSLATE TYPE "atomN" "CHARMM-atomN"

WRITE COOR PDB NAME "my-dnas".PDB

Dear journeyman ,
I try to search the google website . And I just find the Vector Markup Language(VML).Could you tell me full address of VML-software ? Thank you ..
yeng-tseng

actually meant VMD -sorry

http://www.ks.uiuc.edu/Research/vmd/

I don't think that "TRANSLATE TYPE ..." is a CHARMM command by itself, but is part of the processing that can be specified via the "READ UNIVersal ..." command, which does the setup for "READ COOR UNIV ..."

The UNIVersal coordinate reader is a general facility that can be setup to read a wide variety of input coordinate formats. I use to read PDB files routinely, as it allows me to read the B-factors directly into WMAIN, which I find very useful.

See io.doc

I have found the convpdb.pl script from the MMTSB toolset to be very useful in editing pdb files for CHARMM. Give it a try if you're still stumped.

http://mmtsb.scripps.edu/software/mmtsbtoolset.html