Dear Hong Sun,
You could read:
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
regards, Francois
> Hello,I am a beginner in amber.Recently I am following one tutorial
> "a Room Temperature Ionic Liquid" .I got two molecule pdb file from
> gaussian software.And then I transfer them into mol2 format using
> antechamer command .I notice that atom name in the mol2 file are
> not the same as the example mol2 file.For example,in acn.mol2 file I
> made(as follows) ,atoms is named by a element name followed by
> sequence number. The same to other molecule file.
>
> 1 N1 5.5860 -7.0430 0.0000 n1 1 ACN -0.375800
> 2 C2 6.6640 -6.0010 0.0000 c1 1 ACN 0.208700
> 3 C3 6.0430 -4.6350 0.0000 c3 1 ACN -0.045000
> 4 H4 6.9530 -4.2210 0.0000 hc 1 ACN 0.070700
> 5 H5 6.2300 -3.6530 0.0000 hc 1 ACN 0.070700
> 6 H6 5.0600 -4.4480 0.0000 hc 1 ACN 0.070700
> But in the example acn.mol2 file,it shows like this way.
>
>
> 1 H1 2.0000 1.0000 -0.0000 hc 1 ACN 0.070700
> 2 C1 2.0000 2.0900 0.0000 c3 1 ACN -0.045000
> 3 H2 1.4860 2.4540 0.8900 hc 1 ACN 0.070700
> 4 H3 1.4860 2.4540 -0.8900 hc 1 ACN 0.070700
> 5 C 3.4270 2.6410 -0.0000 c1 1 ACN 0.208700
> 6 N 4.7330 3.2140 -0.0300 n1 1 ACN -0.375800
>
> Besides,for the bmi.mol2 file,there exists some unique atom name
> such as ND1 and CE1 which I can not found in my file.I am curious
> about the naming method of this antechamber command.And will it
> bring something different in my calculation?Can it find suitable
> force field parameter for different atom name?
>
> And I have made changes for atom name in the pdb file responding to
> mol2 file.It seems there is some specific requirements for the pdb
> format.For example,if I make a larger spacing distance between O1
> and chc in the following file,it gave error information about not
> finding a proper residue name while I use loadpdb command.Is there
> some notation about the pdb file format?
>
> 6 ATOM 1 O1 chc A 1 43.509 12.032 1.280 1 0
> 7 ATOM 2 N2 chc A 1 40.618 10.274 2.915 1 0
> 8 ATOM 3 C3 chc A 1 41.379 11.316 2.081 1 0
> 9 ATOM 4 C4 chc A 1 40.144 10.886 4.195 1 0
> 10 ATOM 5 C5 chc A 1 41.465 9.063 3.224 1 0
> 11 ATOM 6 C6 chc A 1 42.849 11.601 2.450 1 0
> 12 ATOM 7 H7 chc A 1 41.404 10.902 1.071 1 0
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Thu Mar 24 2016 - 02:30:03 PDT
