From: Satyavani Vemparala (vani_at_VITAE.CMM.UPENN.EDU)
Date: Mon Feb 09 2004 - 15:14:02 CST
Hello:
I am new to NAMD and i had a problem trying to guess coordinates of
hydrogens and generating pdb and psf files from two different segments of
protein & alcohol atoms.
I have a protein and an alcohol molecule, and i made two seperate pdb
files for these. Then i modified the topology file to include the bonding
and residue information of the alcohol. Now when i use the psf gen to
guess coordinates and write combined pdb and psf files, it does it but
also at the end of the protein, includes some dummy atoms all with
coordinates at the origin!
Has it something to do with the lines:
DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
DEFA FIRS NTER LAST CTER
in the CHRMM topology files? is the PSF generatoe expecting that the
second segment is also a protein and trying to attach?
Has anybody else faced this issue, and can anyone suggest a solution to
that?
my script to generate combined PSF & PDB files:
package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U1 {pdb protein.pdb}
coordpdb protein.pdb U1
segment U2 {pdb alcohol.pdb}
coordpdb alcohol.pdb U2
guesscoord
writepdb pro-alc.pdb
writepsf pro-alc.psf
------------------------
MODIFICATION IN TOPOLOGY FILES:
-------------------------------
!-----------------ALCOHOLS-------------------------
! ETHANOL
! =====================
! HA1 HB1
! | |
! HA3-CA1-CB1-OL1-HL1
! | |
! HA2 HB2
!
RESI EOH 0.00
GROUP
ATOM CA1 CT3 -0.27
ATOM HA1 HA 0.09
ATOM HA2 HA 0.09
ATOM HA3 HA 0.09
ATOM CB1 CT2 0.05
ATOM HB1 HA 0.09
ATOM HB2 HA 0.09
ATOM OL1 OH1 -0.66
ATOM HO1 H 0.43
BOND CA1 HA1 CA1 HA2 CA1 HA3 CA1 CB1
BOND CB1 HB1 CB1 HB2
BOND OL1 CB1
BOND OL1 HO1
AUTO ANGLES DIHE
Thanks
Vani
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