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<BLOCKQUOTE id=0><LABEL id=HbSession SessionId="1341237439"></LABEL>
<DIV><FONT face=Arial size=2>Dear gmx users:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am really stuck in my project. I am modeling a
carbon nanotube - protein system and I can not figure out how to set the
topology files for the CNT (carbon nanotube). All I have is a PDB like file
for the CNT and for the protein.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>By reading past messages on the GMX discussion
list it seems that I have to include some extra information in the ffgmx.*
files, particularly the ffgmx.n2t file but in order to do this I need to
know the meaning of the fields of this file which I copy below.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I will appreciate very much if anyone can shine
some light into my darkness.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Much obliged,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>ffgmx.n2t:</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>O O
1
C
; CARBONYL
OXYGEN (C=O)<BR>O OM
1
C
; CARBOXYL
OXYGEN (CO-)<BR>O OA
2 C
H
; HYDROXYL
OXYGEN (OH)<BR>O OW
2
H H
; WATER OXYGEN<BR>N
N 3
H C
C
; PEPTIDE NITROGEN (N OR NH)<BR>N
NT 3 H
H
C
; TERMINAL NITROGEN (NH2)<BR>N
NL 4 C
H H
H ; TERMINAL NITROGEN
(NH3)<BR>N NR5 2
C
C
; AROMATIC N (5-RING,2 BONDS)<BR>N NR5*
3 C C
H
; AROMATIC N (5-RING,3 BONDS)<BR>N
NP 3 C
C
FE ;
PORPHYRIN NITROGEN<BR>C C
3 C
O
*
; BARE CARBON (PEPTIDE,C=O,C-N)<BR>; Note that order is importante here
because of wildcards.<BR>C C3
4 H
H H
* ; ALIPHATIC CH3
GROUP<BR>C C2
4
H H
C * ;
ALIPHATIC CH2 GROUP<BR>C C1
4 H
C *
* ; ALIPHATIC CH
GROUP<BR>C CB
3 C
C
C
; BARE CARBON (5-,6-RING)<BR>H H
1 N
; HYDROGEN BONDED TO NITROGEN<BR>H HO
1 O
; HYDROXYL HYDROGEN<BR>H
HW 1 OW
; WATER HYDROGEN<BR>H HS
1 S
; HYDROGEN BONDED TO SULFUR <BR>H HC
1
C ;
HYDROGEN BONDED TO CARBON<BR></FONT></DIV>
<DIV><FONT face=Arial size=2>______________________________________<BR>Dr.
Ramón Garduño-Juárez<BR>Centro de Ciencias Físicas, UNAM<BR>México<BR>Phone
(777)3291749, (55)56227749<BR>FAX (777)3291775,
(55)56227775</FONT></DIV></BLOCKQUOTE>
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