[gmx-users] David, pls help me with "pdb2gmx"
Yinghong
xieyh at hkusua.hku.hk
Tue May 25 01:15:59 CEST 2004
Dear all:
This problem is related to the simulation of sugar (carbohydrate). When executing "pdb2gmx" command, the fatal error as ""Atom O in residue AGC 1 not found in rtp entry with 14 atoms while sorting atoms." happened.
My 'pdb' file is downloaded from website, and I myself defined the corresponding rtp part in the 'ffgmx.rtp' file. Both of them are just as the follows:
=================***.pdb================================
(Assuming this whole structure contains only one AGC residue)
ATOM 1 C1 AGC 1 1.803 -0.843 0.163 0.00 0.00 C1
ATOM 2 C2 AGC 1 1.161 -0.633 1.531 0.00 0.00 C2
ATOM 3 C3 AGC 1 -0.346 -0.827 1.489 0.00 0.00 C3
ATOM 4 C4 AGC 1 -0.954 -0.008 0.373 0.00 0.00 C4
ATOM 5 C5 AGC 1 -0.250 -0.325 -0.946 0.00 0.00 C5
ATOM 6 C6 AGC 1 -0.755 0.452 -2.142 0.00 0.00 C6
ATOM 7 O2 AGC 1 1.739 -1.554 2.447 0.00 0.00 OH2
ATOM 8 O3 AGC 1 -0.898 -0.399 2.740 0.00 0.00 OH3
ATOM 9 O5 AGC 1 1.141 0.002 -0.787 0.00 0.00 O10
ATOM 10 O6 AGC 1 -0.625 1.853 -1.957 0.00 0.00 OH6
ATOM 11 O1 AGC 1 1.763 -2.177 -0.328 0.00 0.00 OH1
==========================================================
#############residue topology parameter(within ffgmx.rtp)###################
[ AGC ]
[ atoms ]
C1 CS1 0.400 0
O1 OA -0.548 0
O5 OS -0.360 1
C5 CS1 0.160 1
C6 CS2 0.150 2
O6 OA -0.548 2
H6 HO 0.398 2
C2 CS1 0.150 3
O2 OA -0.548 3
H2 HO 0.398 3
C3 CS1 0.150 4
O3 OA -0.548 4
H3 HO 0.398 4
C4 CS1 0.160 5
[ bonds ]
..
..
..
#################################################################
In the rtp file, three hydrogens H2, H3, H6 are added, which are all the hydrogens in the "-OH". And, the "aminoacid.dat" & "ffgmx.hdb" files are also being modified.
I have tried lots of ways, however, this problem can not yet be solved.
Waiting for your precious suggestion!
Thanks in advance!
Xie YH
HongKong University
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