[gmx-users] water molecule not settled, is due to the change in the form of the box?

Andrey V Golovin golovin at genebee.msu.su
Thu Feb 10 10:18:54 CET 2005

Dear Florian,

If OPLS force field is ok to you, than you may get it from contribution
section and i putted link there whit sed script that fix name of
resides. it looks like:

sed -e 's/  A /DADE/' -e 's/  G /DGUA/' -e 's/  C /DCYT/' -e 's/  C /DCYT/' -e 's/  T /DTHY/' -e 's/OP1/O1P/' -e 's/OP2/O2P/'  ${MOL}.pdb> ${MOL}_rp.pdb

just do: export MOL="mypdbname" and run it.
FH> Hi,

>> I'm doing NPT md on my system, a small drug non covalently linked to
>> DNA, and I already performed 8.5 ns simulation.

FH> I want to simulate a piece of DNA too, but i^m not able to do the transfer
FH> from pdb (from a cyrstal structure) to a gromacs topology and coordinate
FH> file.

FH> Do you have perhaps a easy howto?

FH> Greetings,

FH> Florian

Best regards, Andrey

Andrey V. Golovin 
Ph.D,Professor assistant    tel: (095) 939-5305  
Bioengineering and 
Bioinformatics Department              
Moscow State University     fax: (095) 939-3181 
119899 Moscow            E-mail: golovin at genebee.msu.su 
Russia                      web: http://rnp-group.genebee.msu.su 

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